Starting phenix.real_space_refine on Sat May 10 10:17:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.map" model { file = "/net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jaq_61300/05_2025/9jaq_61300.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.094 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 46 5.16 5 C 3886 2.51 5 N 970 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5998 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2999 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 9, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2999 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 9, 'TRANS': 358} Chain breaks: 1 Time building chain proxies: 4.01, per 1000 atoms: 0.67 Number of scatterers: 5998 At special positions: 0 Unit cell: (118.976, 69.056, 84.032, 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 46 16.00 O 1096 8.00 N 970 7.00 C 3886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 62 " distance=2.03 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: 1.30 Conformation dependent library (CDL) restraints added in 835.7 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 56.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 4.606A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.879A pdb=" N ASP A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.509A pdb=" N VAL A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 170 through 183 removed outlier: 4.007A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 203 through 213 removed outlier: 5.294A pdb=" N PHE A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 208 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 293 through 310 removed outlier: 5.175A pdb=" N ASP A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 342 removed outlier: 6.331A pdb=" N GLY A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N MET A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.547A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.770A pdb=" N SER A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 417 Processing helix chain 'B' and resid 14 through 28 removed outlier: 4.606A pdb=" N THR B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 84 through 100 removed outlier: 3.881A pdb=" N ASP B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.509A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.006A pdb=" N ILE B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 removed outlier: 5.292A pdb=" N PHE B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP B 208 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 293 through 310 removed outlier: 5.174A pdb=" N ASP B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 342 removed outlier: 6.332A pdb=" N GLY B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N MET B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.547A pdb=" N LEU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.769A pdb=" N SER B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.769A pdb=" N SER B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 189 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 187 through 189 current: chain 'A' and resid 192 through 194 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 192 through 194 current: chain 'A' and resid 231 through 238 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 231 through 238 current: chain 'A' and resid 241 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 241 through 248 current: chain 'A' and resid 253 through 257 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 253 through 257 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 281 through 283 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 187 through 189 current: chain 'B' and resid 192 through 194 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 192 through 194 current: chain 'B' and resid 231 through 238 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 231 through 238 current: chain 'B' and resid 241 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 241 through 248 current: chain 'B' and resid 253 through 257 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 253 through 257 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 281 through 283 No H-bonds generated for sheet with id=AA2 244 hydrogen bonds defined for protein. 708 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: 1.39 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1844 1.34 - 1.46: 1557 1.46 - 1.58: 2675 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 6142 Sorted by residual: bond pdb=" C ILE B 12 " pdb=" N PRO B 13 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" CG LEU A 338 " pdb=" CD1 LEU A 338 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB GLN B 180 " pdb=" CG GLN B 180 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" C ILE A 12 " pdb=" N PRO A 13 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 bond pdb=" N GLU A 91 " pdb=" CA GLU A 91 " ideal model delta sigma weight residual 1.456 1.470 -0.014 1.33e-02 5.65e+03 1.08e+00 ... (remaining 6137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7992 1.53 - 3.05: 257 3.05 - 4.58: 18 4.58 - 6.11: 5 6.11 - 7.63: 2 Bond angle restraints: 8274 Sorted by residual: angle pdb=" N GLU B 325 " pdb=" CA GLU B 325 " pdb=" C GLU B 325 " ideal model delta sigma weight residual 110.80 118.43 -7.63 2.13e+00 2.20e-01 1.28e+01 angle pdb=" N GLU A 325 " pdb=" CA GLU A 325 " pdb=" C GLU A 325 " ideal model delta sigma weight residual 110.80 118.30 -7.50 2.13e+00 2.20e-01 1.24e+01 angle pdb=" C SER B 289 " pdb=" N VAL B 290 " pdb=" CA VAL B 290 " ideal model delta sigma weight residual 121.97 118.10 3.87 1.80e+00 3.09e-01 4.63e+00 angle pdb=" N GLU B 91 " pdb=" CA GLU B 91 " pdb=" C GLU B 91 " ideal model delta sigma weight residual 113.28 110.69 2.59 1.22e+00 6.72e-01 4.52e+00 angle pdb=" C SER A 289 " pdb=" N VAL A 290 " pdb=" CA VAL A 290 " ideal model delta sigma weight residual 121.97 118.20 3.77 1.80e+00 3.09e-01 4.39e+00 ... (remaining 8269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 3216 16.33 - 32.66: 352 32.66 - 48.99: 64 48.99 - 65.32: 12 65.32 - 81.64: 10 Dihedral angle restraints: 3654 sinusoidal: 1482 harmonic: 2172 Sorted by residual: dihedral pdb=" CA LYS A 59 " pdb=" C LYS A 59 " pdb=" N VAL A 60 " pdb=" CA VAL A 60 " ideal model delta harmonic sigma weight residual 180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS B 59 " pdb=" C LYS B 59 " pdb=" N VAL B 60 " pdb=" CA VAL B 60 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASP B 248 " pdb=" C ASP B 248 " pdb=" N LYS B 249 " pdb=" CA LYS B 249 " ideal model delta harmonic sigma weight residual 180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 652 0.043 - 0.086: 232 0.086 - 0.129: 15 0.129 - 0.172: 7 0.172 - 0.214: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" CA GLU B 325 " pdb=" N GLU B 325 " pdb=" C GLU B 325 " pdb=" CB GLU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 325 " pdb=" N GLU A 325 " pdb=" C GLU A 325 " pdb=" CB GLU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE B 246 " pdb=" CA ILE B 246 " pdb=" CG1 ILE B 246 " pdb=" CG2 ILE B 246 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 905 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 342 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 343 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 342 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 343 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 343 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 344 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.019 5.00e-02 4.00e+02 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 642 2.74 - 3.28: 6004 3.28 - 3.82: 9736 3.82 - 4.36: 12735 4.36 - 4.90: 21296 Nonbonded interactions: 50413 Sorted by model distance: nonbonded pdb=" O CYS A 408 " pdb=" OG1 THR A 412 " model vdw 2.200 3.040 nonbonded pdb=" O CYS B 408 " pdb=" OG1 THR B 412 " model vdw 2.202 3.040 nonbonded pdb=" O LYS A 351 " pdb=" OG1 THR A 355 " model vdw 2.213 3.040 nonbonded pdb=" O LYS B 351 " pdb=" OG1 THR B 355 " model vdw 2.214 3.040 nonbonded pdb=" O ALA A 182 " pdb=" OG SER A 185 " model vdw 2.245 3.040 ... (remaining 50408 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: 0.03 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.720 Find NCS groups from input model: 0.110 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:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.005 0.036 6144 Z= 0.221 Angle : 0.625 7.632 8278 Z= 0.365 Chirality : 0.041 0.214 908 Planarity : 0.004 0.045 1032 Dihedral : 14.517 81.644 2244 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.69 % Favored : 91.76 % Rotamer: Outliers : 0.29 % Allowed : 6.89 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.25), residues: 728 helix: -1.75 (0.22), residues: 358 sheet: -3.16 (0.48), residues: 72 loop : -2.58 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 399 HIS 0.003 0.001 HIS A 269 PHE 0.012 0.002 PHE A 335 TYR 0.009 0.001 TYR A 189 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.11490 ( 238) hydrogen bonds : angle 6.54584 ( 708) SS BOND : bond 0.00146 ( 2) SS BOND : angle 3.23657 ( 4) covalent geometry : bond 0.00502 ( 6142) covalent geometry : angle 0.62158 ( 8274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.734 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 1.2856 time to fit residues: 195.6839 Evaluate side-chains 96 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 262 ASN A 268 HIS A 295 ASN B 180 GLN B 262 ASN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.202689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158173 restraints weight = 6032.457| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.23 r_work: 0.3558 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6144 Z= 0.127 Angle : 0.586 9.733 8278 Z= 0.301 Chirality : 0.039 0.134 908 Planarity : 0.004 0.036 1032 Dihedral : 4.462 14.564 790 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.79 % Allowed : 16.13 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.29), residues: 728 helix: -0.28 (0.27), residues: 352 sheet: -2.59 (0.53), residues: 70 loop : -2.24 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.005 0.001 HIS A 268 PHE 0.009 0.001 PHE A 193 TYR 0.008 0.001 TYR B 189 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 238) hydrogen bonds : angle 4.82624 ( 708) SS BOND : bond 0.00858 ( 2) SS BOND : angle 3.48911 ( 4) covalent geometry : bond 0.00294 ( 6142) covalent geometry : angle 0.58140 ( 8274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.627 Fit side-chains REVERT: A 73 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 171 ASN cc_start: 0.6946 (t0) cc_final: 0.6671 (m-40) REVERT: A 250 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7025 (tmmm) REVERT: B 73 GLU cc_start: 0.7763 (mp0) cc_final: 0.7487 (mp0) REVERT: B 171 ASN cc_start: 0.6899 (t0) cc_final: 0.6650 (m-40) REVERT: B 211 MET cc_start: 0.5875 (mmm) cc_final: 0.5604 (mmm) REVERT: B 250 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.6698 (tmmm) REVERT: B 268 HIS cc_start: 0.7872 (t70) cc_final: 0.7448 (m90) outliers start: 19 outliers final: 4 residues processed: 107 average time/residue: 1.1257 time to fit residues: 126.5421 Evaluate side-chains 99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 250 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.203386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159864 restraints weight = 6073.736| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.99 r_work: 0.3528 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.110 Angle : 0.525 8.322 8278 Z= 0.274 Chirality : 0.038 0.128 908 Planarity : 0.004 0.034 1032 Dihedral : 4.240 12.712 790 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.69 % Allowed : 15.54 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.30), residues: 728 helix: 0.24 (0.28), residues: 356 sheet: -2.34 (0.56), residues: 70 loop : -1.85 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 399 HIS 0.002 0.000 HIS A 241 PHE 0.007 0.001 PHE A 193 TYR 0.013 0.001 TYR A 183 ARG 0.002 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 238) hydrogen bonds : angle 4.57845 ( 708) SS BOND : bond 0.00172 ( 2) SS BOND : angle 3.35383 ( 4) covalent geometry : bond 0.00252 ( 6142) covalent geometry : angle 0.52015 ( 8274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.757 Fit side-chains REVERT: A 90 LYS cc_start: 0.8386 (mttp) cc_final: 0.8072 (mptp) REVERT: A 171 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6780 (m-40) REVERT: A 250 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.6867 (tmmm) REVERT: A 268 HIS cc_start: 0.7819 (t70) cc_final: 0.7350 (m90) REVERT: A 303 ARG cc_start: 0.7301 (mtm180) cc_final: 0.6686 (mmm-85) REVERT: B 73 GLU cc_start: 0.7967 (mp0) cc_final: 0.7629 (mp0) REVERT: B 90 LYS cc_start: 0.8372 (mttp) cc_final: 0.8067 (mptp) REVERT: B 250 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.6585 (tmmm) REVERT: B 268 HIS cc_start: 0.7842 (t70) cc_final: 0.7383 (m90) REVERT: B 303 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6674 (mmm-85) outliers start: 32 outliers final: 13 residues processed: 114 average time/residue: 0.9571 time to fit residues: 115.7472 Evaluate side-chains 109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 33 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.200420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.156253 restraints weight = 6114.357| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.10 r_work: 0.3566 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6144 Z= 0.127 Angle : 0.533 7.863 8278 Z= 0.274 Chirality : 0.038 0.131 908 Planarity : 0.004 0.035 1032 Dihedral : 4.195 13.263 790 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.96 % Allowed : 17.30 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.30), residues: 728 helix: 0.33 (0.28), residues: 356 sheet: -2.09 (0.58), residues: 70 loop : -1.62 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 234 TYR 0.016 0.001 TYR B 183 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 238) hydrogen bonds : angle 4.52029 ( 708) SS BOND : bond 0.00087 ( 2) SS BOND : angle 3.10517 ( 4) covalent geometry : bond 0.00297 ( 6142) covalent geometry : angle 0.52852 ( 8274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.723 Fit side-chains REVERT: A 73 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: A 250 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.6863 (tmmm) REVERT: A 268 HIS cc_start: 0.7854 (t70) cc_final: 0.7412 (m90) REVERT: A 303 ARG cc_start: 0.7377 (mtm180) cc_final: 0.6787 (mmm-85) REVERT: B 73 GLU cc_start: 0.8042 (mp0) cc_final: 0.7654 (mp0) REVERT: B 90 LYS cc_start: 0.8351 (mttp) cc_final: 0.8092 (mptp) REVERT: B 250 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.6597 (tmmm) REVERT: B 268 HIS cc_start: 0.7855 (t70) cc_final: 0.7408 (m90) REVERT: B 287 ARG cc_start: 0.6616 (mpp-170) cc_final: 0.6369 (mpp-170) REVERT: B 303 ARG cc_start: 0.7344 (mtm180) cc_final: 0.6783 (mmm-85) outliers start: 27 outliers final: 14 residues processed: 115 average time/residue: 0.9747 time to fit residues: 118.6433 Evaluate side-chains 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.199752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155398 restraints weight = 6074.607| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.09 r_work: 0.3547 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6144 Z= 0.156 Angle : 0.551 7.757 8278 Z= 0.286 Chirality : 0.039 0.130 908 Planarity : 0.004 0.037 1032 Dihedral : 4.273 14.247 790 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.81 % Allowed : 18.33 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.31), residues: 728 helix: 0.33 (0.28), residues: 354 sheet: -1.99 (0.61), residues: 70 loop : -1.44 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 399 HIS 0.003 0.001 HIS B 269 PHE 0.008 0.001 PHE A 234 TYR 0.016 0.001 TYR B 183 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 238) hydrogen bonds : angle 4.60714 ( 708) SS BOND : bond 0.00182 ( 2) SS BOND : angle 2.98433 ( 4) covalent geometry : bond 0.00369 ( 6142) covalent geometry : angle 0.54746 ( 8274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: A 90 LYS cc_start: 0.8388 (mttp) cc_final: 0.8086 (mptp) REVERT: A 171 ASN cc_start: 0.6888 (t0) cc_final: 0.6589 (m-40) REVERT: A 250 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.6958 (tmmm) REVERT: A 268 HIS cc_start: 0.7888 (t70) cc_final: 0.7309 (m90) REVERT: A 287 ARG cc_start: 0.6901 (mpp-170) cc_final: 0.6693 (mpp-170) REVERT: A 303 ARG cc_start: 0.7420 (mtm180) cc_final: 0.6858 (mmm-85) REVERT: B 73 GLU cc_start: 0.8091 (mp0) cc_final: 0.7641 (mp0) REVERT: B 196 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6801 (ptt-90) REVERT: B 211 MET cc_start: 0.5866 (mmm) cc_final: 0.5612 (mmm) REVERT: B 250 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.6718 (tmmm) REVERT: B 303 ARG cc_start: 0.7421 (mtm180) cc_final: 0.6837 (mmm-85) outliers start: 26 outliers final: 16 residues processed: 116 average time/residue: 0.9768 time to fit residues: 119.8739 Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.202206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157639 restraints weight = 5941.251| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.14 r_work: 0.3523 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6144 Z= 0.125 Angle : 0.536 9.718 8278 Z= 0.278 Chirality : 0.039 0.178 908 Planarity : 0.004 0.036 1032 Dihedral : 4.198 16.207 790 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.96 % Allowed : 19.21 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.31), residues: 728 helix: 0.49 (0.28), residues: 356 sheet: -1.76 (0.63), residues: 70 loop : -1.47 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 399 HIS 0.004 0.001 HIS A 241 PHE 0.007 0.001 PHE A 234 TYR 0.016 0.001 TYR B 183 ARG 0.002 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 238) hydrogen bonds : angle 4.53554 ( 708) SS BOND : bond 0.00126 ( 2) SS BOND : angle 2.96064 ( 4) covalent geometry : bond 0.00289 ( 6142) covalent geometry : angle 0.53242 ( 8274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.632 Fit side-chains REVERT: A 73 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 90 LYS cc_start: 0.8327 (mttp) cc_final: 0.8073 (mptp) REVERT: A 171 ASN cc_start: 0.6863 (t0) cc_final: 0.6622 (m-40) REVERT: A 250 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.6983 (tmmm) REVERT: A 287 ARG cc_start: 0.6886 (mpp-170) cc_final: 0.6656 (mpp-170) REVERT: A 303 ARG cc_start: 0.7460 (mtm180) cc_final: 0.6883 (mmm-85) REVERT: B 73 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 211 MET cc_start: 0.5798 (mmm) cc_final: 0.5391 (mmm) REVERT: B 250 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.6642 (tmmm) REVERT: B 303 ARG cc_start: 0.7461 (mtm180) cc_final: 0.6865 (mmm-85) outliers start: 27 outliers final: 13 residues processed: 115 average time/residue: 0.9973 time to fit residues: 121.3298 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.198438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154320 restraints weight = 6002.661| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.82 r_work: 0.3501 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6144 Z= 0.162 Angle : 0.590 10.916 8278 Z= 0.302 Chirality : 0.040 0.202 908 Planarity : 0.004 0.036 1032 Dihedral : 4.323 16.513 790 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.81 % Allowed : 20.82 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 728 helix: 0.44 (0.27), residues: 356 sheet: -1.80 (0.62), residues: 70 loop : -1.48 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 399 HIS 0.004 0.001 HIS A 241 PHE 0.030 0.001 PHE B 107 TYR 0.017 0.001 TYR B 183 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 238) hydrogen bonds : angle 4.64245 ( 708) SS BOND : bond 0.00247 ( 2) SS BOND : angle 2.96225 ( 4) covalent geometry : bond 0.00380 ( 6142) covalent geometry : angle 0.58650 ( 8274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.740 Fit side-chains REVERT: A 73 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 90 LYS cc_start: 0.8214 (mttp) cc_final: 0.7947 (mptp) REVERT: A 250 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7045 (tmmm) REVERT: A 287 ARG cc_start: 0.6931 (mpp-170) cc_final: 0.6680 (mpp-170) REVERT: A 303 ARG cc_start: 0.7463 (mtm180) cc_final: 0.6975 (mtp85) REVERT: B 73 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 90 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7840 (mtmm) REVERT: B 250 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.6769 (tmmm) REVERT: B 303 ARG cc_start: 0.7473 (mtm180) cc_final: 0.6966 (mtp85) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.9513 time to fit residues: 113.9443 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** 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 = 0.4304 r_free = 0.4304 target = 0.201659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157731 restraints weight = 5948.170| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.84 r_work: 0.3550 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6144 Z= 0.123 Angle : 0.561 10.070 8278 Z= 0.284 Chirality : 0.040 0.221 908 Planarity : 0.004 0.036 1032 Dihedral : 4.181 16.279 790 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.23 % Allowed : 21.11 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.31), residues: 728 helix: 0.67 (0.28), residues: 354 sheet: -1.65 (0.63), residues: 70 loop : -1.31 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 242 HIS 0.004 0.001 HIS A 241 PHE 0.041 0.001 PHE B 107 TYR 0.016 0.001 TYR B 183 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 238) hydrogen bonds : angle 4.54234 ( 708) SS BOND : bond 0.00141 ( 2) SS BOND : angle 2.99268 ( 4) covalent geometry : bond 0.00284 ( 6142) covalent geometry : angle 0.55680 ( 8274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 171 ASN cc_start: 0.6773 (t0) cc_final: 0.6491 (m-40) REVERT: A 250 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.6985 (tmmm) REVERT: A 287 ARG cc_start: 0.6933 (mpp-170) cc_final: 0.6682 (mpp-170) REVERT: A 303 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7055 (mtp85) REVERT: B 73 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: B 303 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7029 (mtp85) outliers start: 22 outliers final: 13 residues processed: 112 average time/residue: 1.0275 time to fit residues: 121.8451 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** 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 = 0.4312 r_free = 0.4312 target = 0.202514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158867 restraints weight = 5973.182| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.83 r_work: 0.3573 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.131 Angle : 0.569 10.269 8278 Z= 0.289 Chirality : 0.040 0.222 908 Planarity : 0.004 0.035 1032 Dihedral : 4.163 16.167 790 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.93 % Allowed : 22.43 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.31), residues: 728 helix: 0.68 (0.27), residues: 354 sheet: -1.69 (0.63), residues: 70 loop : -1.29 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 399 HIS 0.004 0.001 HIS B 241 PHE 0.037 0.001 PHE A 107 TYR 0.019 0.001 TYR B 183 ARG 0.002 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 238) hydrogen bonds : angle 4.55676 ( 708) SS BOND : bond 0.00213 ( 2) SS BOND : angle 2.95266 ( 4) covalent geometry : bond 0.00305 ( 6142) covalent geometry : angle 0.56557 ( 8274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: A 171 ASN cc_start: 0.6796 (t0) cc_final: 0.6506 (m-40) REVERT: A 250 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7029 (tmmm) REVERT: A 303 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7083 (mtp85) REVERT: B 73 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 90 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7801 (mttp) REVERT: B 211 MET cc_start: 0.5857 (mmm) cc_final: 0.5606 (mmm) REVERT: B 303 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7082 (mtp85) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 1.0304 time to fit residues: 116.5719 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** 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 = 0.4319 r_free = 0.4319 target = 0.203090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159142 restraints weight = 6002.964| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.93 r_work: 0.3527 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.137 Angle : 0.577 10.267 8278 Z= 0.293 Chirality : 0.040 0.226 908 Planarity : 0.004 0.036 1032 Dihedral : 4.200 16.128 790 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.64 % Allowed : 22.14 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 728 helix: 0.67 (0.28), residues: 354 sheet: -1.73 (0.63), residues: 70 loop : -1.29 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 242 HIS 0.004 0.001 HIS A 241 PHE 0.039 0.001 PHE A 107 TYR 0.019 0.001 TYR A 183 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 238) hydrogen bonds : angle 4.58804 ( 708) SS BOND : bond 0.00223 ( 2) SS BOND : angle 2.89607 ( 4) covalent geometry : bond 0.00322 ( 6142) covalent geometry : angle 0.57316 ( 8274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 171 ASN cc_start: 0.6815 (t0) cc_final: 0.6532 (m-40) REVERT: A 250 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7005 (tmmm) REVERT: A 303 ARG cc_start: 0.7526 (mtm180) cc_final: 0.7104 (mtp85) REVERT: B 73 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 90 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7828 (mttp) REVERT: B 303 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7084 (mtp85) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.9885 time to fit residues: 111.8725 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.202792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159103 restraints weight = 6089.416| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.87 r_work: 0.3512 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6144 Z= 0.141 Angle : 0.579 10.375 8278 Z= 0.295 Chirality : 0.040 0.228 908 Planarity : 0.004 0.035 1032 Dihedral : 4.209 15.858 790 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.37 % Allowed : 20.67 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.31), residues: 728 helix: 0.66 (0.28), residues: 354 sheet: -1.72 (0.62), residues: 70 loop : -1.27 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 399 HIS 0.004 0.001 HIS B 241 PHE 0.025 0.001 PHE B 107 TYR 0.018 0.001 TYR A 183 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 238) hydrogen bonds : angle 4.61613 ( 708) SS BOND : bond 0.00220 ( 2) SS BOND : angle 2.90213 ( 4) covalent geometry : bond 0.00331 ( 6142) covalent geometry : angle 0.57585 ( 8274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.92 seconds wall clock time: 75 minutes 23.06 seconds (4523.06 seconds total)