Starting phenix.real_space_refine on Tue Feb 3 18:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.map" model { file = "/net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wt2_66215/02_2026/9wt2_66215.cif" } resolution = 3.12 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= 0.000 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4156 2.51 5 N 1010 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3160 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 1 Chain: "B" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3160 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 1 Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6320 At special positions: 0 Unit cell: (73.336, 94.76, 75.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1114 8.00 N 1010 7.00 C 4156 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: 0.48 Conformation dependent library (CDL) restraints added in 150.4 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.651A pdb=" N LEU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 45 through 74 removed outlier: 3.525A pdb=" N GLN A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 95 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.817A pdb=" N GLY A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.726A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 removed outlier: 3.973A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.990A pdb=" N VAL A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.034A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.863A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 231 " --> pdb=" O TRP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 258 through 291 removed outlier: 3.927A pdb=" N MET A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 357 removed outlier: 3.618A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Proline residue: A 345 - end of helix removed outlier: 3.794A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.862A pdb=" N CYS A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.910A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.760A pdb=" N GLU B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 74 removed outlier: 3.565A pdb=" N ILE B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 removed outlier: 3.651A pdb=" N SER B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.730A pdb=" N GLY B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.631A pdb=" N CYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 125 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 159 removed outlier: 3.932A pdb=" N SER B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 164 through 187 removed outlier: 3.568A pdb=" N PHE B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.874A pdb=" N VAL B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.060A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.917A pdb=" N THR B 231 " --> pdb=" O TRP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 291 removed outlier: 4.186A pdb=" N MET B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 321 Processing helix chain 'B' and resid 327 through 357 removed outlier: 3.708A pdb=" N ILE B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Proline residue: B 345 - end of helix removed outlier: 3.671A pdb=" N GLY B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.757A pdb=" N CYS B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 380 Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.752A pdb=" N ILE B 387 " --> pdb=" O PRO B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 414 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' 495 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1906 1.34 - 1.46: 1575 1.46 - 1.58: 2947 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6494 Sorted by residual: bond pdb=" CB GLU B 219 " pdb=" CG GLU B 219 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C PRO B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.68e-01 bond pdb=" C VAL B 66 " pdb=" O VAL B 66 " ideal model delta sigma weight residual 1.242 1.233 0.009 1.13e-02 7.83e+03 6.52e-01 bond pdb=" C PRO A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.02e-01 bond pdb=" CG ARG A 418 " pdb=" CD ARG A 418 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.01e-01 ... (remaining 6489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 8678 1.98 - 3.96: 129 3.96 - 5.94: 15 5.94 - 7.92: 8 7.92 - 9.91: 4 Bond angle restraints: 8834 Sorted by residual: angle pdb=" CA GLU B 219 " pdb=" CB GLU B 219 " pdb=" CG GLU B 219 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N SER A 162 " pdb=" CA SER A 162 " pdb=" C SER A 162 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" CB GLU B 219 " pdb=" CG GLU B 219 " pdb=" CD GLU B 219 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 angle pdb=" CA LEU B 234 " pdb=" CB LEU B 234 " pdb=" CG LEU B 234 " ideal model delta sigma weight residual 116.30 126.21 -9.91 3.50e+00 8.16e-02 8.01e+00 angle pdb=" CA LEU B 151 " pdb=" CB LEU B 151 " pdb=" CG LEU B 151 " ideal model delta sigma weight residual 116.30 126.16 -9.86 3.50e+00 8.16e-02 7.93e+00 ... (remaining 8829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 3123 16.67 - 33.35: 412 33.35 - 50.02: 120 50.02 - 66.70: 28 66.70 - 83.37: 7 Dihedral angle restraints: 3690 sinusoidal: 1342 harmonic: 2348 Sorted by residual: dihedral pdb=" CA GLY A 247 " pdb=" C GLY A 247 " pdb=" N GLN A 248 " pdb=" CA GLN A 248 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY B 247 " pdb=" C GLY B 247 " pdb=" N GLN B 248 " pdb=" CA GLN B 248 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TRP A 227 " pdb=" C TRP A 227 " pdb=" N VAL A 228 " pdb=" CA VAL A 228 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 667 0.034 - 0.068: 263 0.068 - 0.101: 52 0.101 - 0.135: 15 0.135 - 0.169: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" CG LEU A 414 " pdb=" CB LEU A 414 " pdb=" CD1 LEU A 414 " pdb=" CD2 LEU A 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CG LEU B 413 " pdb=" CB LEU B 413 " pdb=" CD1 LEU B 413 " pdb=" CD2 LEU B 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 995 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 249 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C PHE A 249 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 249 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 250 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 118 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 119 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 344 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 345 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.024 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 2879 2.95 - 3.44: 6958 3.44 - 3.93: 10873 3.93 - 4.41: 12577 4.41 - 4.90: 20215 Nonbonded interactions: 53502 Sorted by model distance: nonbonded pdb=" N GLU B 219 " pdb=" OE1 GLU B 219 " model vdw 2.468 3.120 nonbonded pdb=" N GLU A 219 " pdb=" OE1 GLU A 219 " model vdw 2.544 3.120 nonbonded pdb=" O SER A 67 " pdb=" OG SER A 71 " model vdw 2.550 3.040 nonbonded pdb=" O GLY A 381 " pdb=" OG SER A 385 " model vdw 2.558 3.040 nonbonded pdb=" O TYR A 391 " pdb=" OG SER A 392 " model vdw 2.561 3.040 ... (remaining 53497 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6494 Z= 0.145 Angle : 0.654 9.906 8834 Z= 0.343 Chirality : 0.038 0.169 998 Planarity : 0.005 0.046 1084 Dihedral : 17.027 83.370 2198 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.95 % Allowed : 30.48 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.29), residues: 820 helix: 0.77 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.22 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 418 TYR 0.014 0.001 TYR B 282 PHE 0.009 0.001 PHE A 14 TRP 0.011 0.001 TRP B 227 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6494) covalent geometry : angle 0.65362 ( 8834) hydrogen bonds : bond 0.19551 ( 495) hydrogen bonds : angle 6.96580 ( 1479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.139 Fit side-chains REVERT: A 41 GLU cc_start: 0.7894 (tt0) cc_final: 0.7366 (pt0) REVERT: A 133 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6294 (mt0) REVERT: A 151 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7913 (tm) REVERT: A 218 GLN cc_start: 0.5626 (OUTLIER) cc_final: 0.4048 (tm-30) REVERT: A 423 ARG cc_start: 0.7412 (tpp80) cc_final: 0.7028 (tpp80) REVERT: B 133 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6157 (mt0) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 0.0655 time to fit residues: 8.6171 Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 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 = 0.4022 r_free = 0.4022 target = 0.180342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148395 restraints weight = 7022.265| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.71 r_work: 0.3521 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6494 Z= 0.145 Angle : 0.579 8.147 8834 Z= 0.295 Chirality : 0.039 0.218 998 Planarity : 0.005 0.047 1084 Dihedral : 7.515 79.943 901 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.80 % Allowed : 25.83 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.30), residues: 820 helix: 1.36 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.78 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 418 TYR 0.012 0.001 TYR B 24 PHE 0.011 0.001 PHE A 412 TRP 0.009 0.001 TRP B 227 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6494) covalent geometry : angle 0.57920 ( 8834) hydrogen bonds : bond 0.05016 ( 495) hydrogen bonds : angle 4.50577 ( 1479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: A 151 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8429 (tm) REVERT: A 288 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7677 (mtm) REVERT: A 329 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8137 (tp) outliers start: 32 outliers final: 13 residues processed: 124 average time/residue: 0.0513 time to fit residues: 8.8698 Evaluate side-chains 113 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.180296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148302 restraints weight = 7022.359| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.71 r_work: 0.3527 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6494 Z= 0.134 Angle : 0.543 8.241 8834 Z= 0.274 Chirality : 0.038 0.137 998 Planarity : 0.004 0.051 1084 Dihedral : 5.264 54.193 888 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.11 % Allowed : 23.72 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.30), residues: 820 helix: 1.56 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.58 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.011 0.001 TYR A 24 PHE 0.011 0.001 PHE A 340 TRP 0.009 0.001 TRP B 227 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6494) covalent geometry : angle 0.54304 ( 8834) hydrogen bonds : bond 0.04406 ( 495) hydrogen bonds : angle 4.27020 ( 1479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.224 Fit side-chains REVERT: A 133 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6811 (mt0) REVERT: A 145 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7338 (mtt) REVERT: A 151 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8438 (tm) REVERT: A 288 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: A 329 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 70 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6860 (tt) REVERT: B 133 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6916 (mt0) REVERT: B 218 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.4137 (tm-30) outliers start: 34 outliers final: 17 residues processed: 125 average time/residue: 0.0602 time to fit residues: 10.4018 Evaluate side-chains 120 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143192 restraints weight = 7074.571| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.73 r_work: 0.3513 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6494 Z= 0.138 Angle : 0.538 7.773 8834 Z= 0.272 Chirality : 0.039 0.268 998 Planarity : 0.004 0.052 1084 Dihedral : 5.058 56.348 886 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.01 % Allowed : 22.52 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.30), residues: 820 helix: 1.66 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.012 0.001 TYR A 24 PHE 0.011 0.001 PHE A 340 TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6494) covalent geometry : angle 0.53792 ( 8834) hydrogen bonds : bond 0.04167 ( 495) hydrogen bonds : angle 4.17493 ( 1479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6702 (tt) REVERT: A 133 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6803 (mt0) REVERT: A 145 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7366 (mtt) REVERT: A 151 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8454 (tm) REVERT: A 288 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7723 (mtm) REVERT: A 329 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 70 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6827 (tt) REVERT: B 133 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: B 175 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 218 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.4171 (tm-30) outliers start: 40 outliers final: 20 residues processed: 127 average time/residue: 0.0588 time to fit residues: 10.2129 Evaluate side-chains 124 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142151 restraints weight = 7218.529| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.76 r_work: 0.3459 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6494 Z= 0.185 Angle : 0.598 11.117 8834 Z= 0.297 Chirality : 0.040 0.157 998 Planarity : 0.005 0.053 1084 Dihedral : 5.157 59.665 886 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.31 % Allowed : 21.92 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.30), residues: 820 helix: 1.67 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.87 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.016 0.001 TYR A 24 PHE 0.012 0.002 PHE A 340 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6494) covalent geometry : angle 0.59798 ( 8834) hydrogen bonds : bond 0.04490 ( 495) hydrogen bonds : angle 4.23549 ( 1479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.137 Fit side-chains REVERT: A 1 MET cc_start: 0.7468 (mtt) cc_final: 0.7262 (mtp) REVERT: A 17 MET cc_start: 0.8327 (mtm) cc_final: 0.7849 (mtm) REVERT: A 70 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6947 (tt) REVERT: A 133 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6800 (mt0) REVERT: A 151 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (tm) REVERT: A 288 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: A 326 SER cc_start: 0.8931 (m) cc_final: 0.8343 (p) REVERT: A 329 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8084 (tp) REVERT: B 70 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6881 (tt) REVERT: B 133 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: B 175 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7812 (tp) REVERT: B 218 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.4212 (tm-30) outliers start: 42 outliers final: 25 residues processed: 131 average time/residue: 0.0567 time to fit residues: 10.3231 Evaluate side-chains 131 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.179014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145813 restraints weight = 7086.548| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.78 r_work: 0.3503 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6494 Z= 0.125 Angle : 0.554 13.111 8834 Z= 0.272 Chirality : 0.039 0.371 998 Planarity : 0.004 0.053 1084 Dihedral : 5.058 56.964 886 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.41 % Allowed : 22.82 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.30), residues: 820 helix: 1.86 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.59 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.011 0.001 TYR A 24 PHE 0.011 0.001 PHE A 340 TRP 0.008 0.001 TRP A 227 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6494) covalent geometry : angle 0.55370 ( 8834) hydrogen bonds : bond 0.04010 ( 495) hydrogen bonds : angle 4.12740 ( 1479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.8250 (mtm) cc_final: 0.7901 (mtm) REVERT: A 70 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6677 (tt) REVERT: A 133 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: A 145 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7341 (mtt) REVERT: A 151 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (tm) REVERT: A 161 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: A 288 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: A 326 SER cc_start: 0.8912 (m) cc_final: 0.8335 (p) REVERT: A 329 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 70 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6846 (tt) REVERT: B 133 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: B 218 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.4240 (tm-30) REVERT: B 306 PHE cc_start: 0.6730 (m-80) cc_final: 0.6256 (t80) outliers start: 36 outliers final: 19 residues processed: 125 average time/residue: 0.0596 time to fit residues: 10.1814 Evaluate side-chains 128 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145532 restraints weight = 7071.251| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.77 r_work: 0.3504 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6494 Z= 0.132 Angle : 0.563 11.908 8834 Z= 0.278 Chirality : 0.038 0.194 998 Planarity : 0.004 0.053 1084 Dihedral : 5.011 54.948 886 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.11 % Allowed : 23.27 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.30), residues: 820 helix: 1.87 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.56 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.020 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.009 0.001 TRP A 227 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6494) covalent geometry : angle 0.56275 ( 8834) hydrogen bonds : bond 0.03956 ( 495) hydrogen bonds : angle 4.09274 ( 1479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6705 (tt) REVERT: A 133 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6750 (mt0) REVERT: A 145 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7318 (mtt) REVERT: A 151 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8421 (tm) REVERT: A 161 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: A 288 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: A 326 SER cc_start: 0.8908 (m) cc_final: 0.8317 (p) REVERT: A 329 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 24 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 70 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6874 (tt) REVERT: B 133 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: B 218 GLN cc_start: 0.5914 (OUTLIER) cc_final: 0.4256 (tm-30) REVERT: B 306 PHE cc_start: 0.6741 (m-80) cc_final: 0.6279 (t80) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.0560 time to fit residues: 9.4101 Evaluate side-chains 128 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146072 restraints weight = 7069.441| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.75 r_work: 0.3514 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6494 Z= 0.134 Angle : 0.574 13.774 8834 Z= 0.283 Chirality : 0.038 0.136 998 Planarity : 0.004 0.053 1084 Dihedral : 4.986 53.394 886 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.41 % Allowed : 23.12 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.30), residues: 820 helix: 1.92 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.59 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.018 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.006 0.001 TRP A 107 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6494) covalent geometry : angle 0.57427 ( 8834) hydrogen bonds : bond 0.03965 ( 495) hydrogen bonds : angle 4.10937 ( 1479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6646 (tt) REVERT: A 133 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: A 145 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7328 (mtt) REVERT: A 151 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8451 (tm) REVERT: A 288 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7650 (mtm) REVERT: A 326 SER cc_start: 0.8925 (m) cc_final: 0.8331 (p) REVERT: A 329 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 24 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: B 70 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6887 (tt) REVERT: B 133 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: B 218 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.4326 (tm-30) REVERT: B 326 SER cc_start: 0.8908 (m) cc_final: 0.8315 (p) outliers start: 36 outliers final: 23 residues processed: 122 average time/residue: 0.0512 time to fit residues: 8.6829 Evaluate side-chains 128 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145440 restraints weight = 7185.414| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.80 r_work: 0.3504 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6494 Z= 0.137 Angle : 0.589 13.159 8834 Z= 0.290 Chirality : 0.038 0.134 998 Planarity : 0.004 0.053 1084 Dihedral : 4.970 52.094 886 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.80 % Allowed : 23.57 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.30), residues: 820 helix: 1.93 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.63 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.018 0.001 TYR A 225 PHE 0.014 0.001 PHE B 412 TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6494) covalent geometry : angle 0.58905 ( 8834) hydrogen bonds : bond 0.03967 ( 495) hydrogen bonds : angle 4.11835 ( 1479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: A 145 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (mtt) REVERT: A 151 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8437 (tm) REVERT: A 288 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: A 326 SER cc_start: 0.8923 (m) cc_final: 0.8316 (p) REVERT: A 329 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 24 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 70 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6918 (tt) REVERT: B 133 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: B 218 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.4153 (tm-30) outliers start: 32 outliers final: 22 residues processed: 115 average time/residue: 0.0602 time to fit residues: 9.3829 Evaluate side-chains 124 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145016 restraints weight = 7100.396| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.78 r_work: 0.3491 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6494 Z= 0.143 Angle : 0.589 12.921 8834 Z= 0.290 Chirality : 0.038 0.136 998 Planarity : 0.004 0.053 1084 Dihedral : 4.960 51.144 886 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.80 % Allowed : 23.27 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.30), residues: 820 helix: 1.84 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.95 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.014 0.001 TYR A 24 PHE 0.011 0.001 PHE A 340 TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6494) covalent geometry : angle 0.58893 ( 8834) hydrogen bonds : bond 0.04006 ( 495) hydrogen bonds : angle 4.11600 ( 1479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: A 145 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7410 (mtt) REVERT: A 151 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8423 (tm) REVERT: A 288 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7631 (mtm) REVERT: A 326 SER cc_start: 0.8939 (m) cc_final: 0.8324 (p) REVERT: A 329 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 24 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: B 70 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6917 (tt) REVERT: B 133 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6846 (mt0) REVERT: B 218 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.4361 (tm-30) REVERT: B 326 SER cc_start: 0.8927 (m) cc_final: 0.8321 (p) outliers start: 32 outliers final: 22 residues processed: 117 average time/residue: 0.0697 time to fit residues: 11.1096 Evaluate side-chains 123 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148906 restraints weight = 7061.742| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.72 r_work: 0.3537 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6494 Z= 0.121 Angle : 0.580 12.687 8834 Z= 0.284 Chirality : 0.037 0.131 998 Planarity : 0.004 0.053 1084 Dihedral : 4.902 50.515 886 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.20 % Allowed : 24.32 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.31 (0.30), residues: 820 helix: 1.93 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.49 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.017 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.006 0.001 TRP A 107 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6494) covalent geometry : angle 0.57969 ( 8834) hydrogen bonds : bond 0.03741 ( 495) hydrogen bonds : angle 4.05107 ( 1479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1315.27 seconds wall clock time: 23 minutes 13.35 seconds (1393.35 seconds total)