Starting phenix.real_space_refine on Thu Oct 22 21:18:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.map" model { file = "/net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wut_66270/10_2026/9wut_66270.cif" } resolution = 3.04 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 135 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 36 5.16 5 C 3591 2.51 5 N 955 2.21 5 O 1004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5587 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2819 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2811 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 23, 'TRANS': 329} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 353, 2811 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 23, 'TRANS': 329} Chain breaks: 3 bond proxies already assigned to first conformer: 2871 Chain: "A" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2758 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 23, 'TRANS': 321} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 345, 2758 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 23, 'TRANS': 321} Chain breaks: 2 bond proxies already assigned to first conformer: 2818 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.40 Number of scatterers: 5587 At special positions: 0 Unit cell: (70.808, 90.848, 100.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 36 16.00 O 1004 8.00 N 955 7.00 C 3591 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: 0.43 Conformation dependent library (CDL) restraints added in 470.0 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 45.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 204 through 218 removed outlier: 3.658A pdb=" N GLU B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.240A pdb=" N GLU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 310 through 330 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.868A pdb=" N TRP B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.799A pdb=" N LEU B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.920A pdb=" N CYS B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.584A pdb=" N LYS B 492 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 517 Processing helix chain 'B' and resid 536 through 549 removed outlier: 3.779A pdb=" N ARG B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.119A pdb=" N ILE A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.665A pdb=" N GLU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 310 through 330 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.938A pdb=" N TRP A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.552A pdb=" N ARG A 470 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 486 removed outlier: 3.939A pdb=" N CYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.733A pdb=" N LYS A 492 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 536 through 549 removed outlier: 3.699A pdb=" N ARG A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.581A pdb=" N ILE A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.731A pdb=" N SER B 255 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AA3, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.553A pdb=" N CYS B 299 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 333 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 193 through 200 removed outlier: 3.696A pdb=" N SER A 255 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.629A pdb=" N ILE A 354 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.946A pdb=" N SER A 402 " --> pdb=" O TYR A 375 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 661 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: 0.76 Time building geometry restraints manager: 0.60 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: 1782 1.34 - 1.46: 1174 1.46 - 1.58: 2713 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5725 Sorted by residual: bond pdb=" C TYR B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.34e+00 bond pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta sigma weight residual 1.479 1.467 0.012 1.56e-02 4.11e+03 6.35e-01 bond pdb=" CB PRO B 220 " pdb=" CG PRO B 220 " ideal model delta sigma weight residual 1.492 1.460 0.032 5.00e-02 4.00e+02 4.13e-01 bond pdb=" CA TYR B 191 " pdb=" C TYR B 191 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.26e-02 6.30e+03 3.42e-01 bond pdb=" CB PRO A 220 " pdb=" CG PRO A 220 " ideal model delta sigma weight residual 1.492 1.464 0.028 5.00e-02 4.00e+02 3.20e-01 ... (remaining 5720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7655 1.51 - 3.02: 101 3.02 - 4.54: 21 4.54 - 6.05: 5 6.05 - 7.56: 1 Bond angle restraints: 7783 Sorted by residual: angle pdb=" N TYR A 191 " pdb=" CA TYR A 191 " pdb=" C TYR A 191 " ideal model delta sigma weight residual 109.81 115.85 -6.04 2.21e+00 2.05e-01 7.46e+00 angle pdb=" N SER A 358 " pdb=" CA SER A 358 " pdb=" C SER A 358 " ideal model delta sigma weight residual 108.34 111.84 -3.50 1.31e+00 5.83e-01 7.13e+00 angle pdb=" CG1 ILE B 203 " pdb=" CB ILE B 203 " pdb=" CG2 ILE B 203 " ideal model delta sigma weight residual 110.70 103.14 7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" CA PHE B 193 " pdb=" C PHE B 193 " pdb=" O PHE B 193 " ideal model delta sigma weight residual 120.27 122.86 -2.59 1.24e+00 6.50e-01 4.38e+00 angle pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" CD PRO A 192 " ideal model delta sigma weight residual 112.00 109.13 2.87 1.40e+00 5.10e-01 4.20e+00 ... (remaining 7778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3107 17.99 - 35.99: 308 35.99 - 53.98: 43 53.98 - 71.97: 5 71.97 - 89.96: 4 Dihedral angle restraints: 3467 sinusoidal: 1403 harmonic: 2064 Sorted by residual: dihedral pdb=" CB GLU B 502 " pdb=" CG GLU B 502 " pdb=" CD GLU B 502 " pdb=" OE1 GLU B 502 " ideal model delta sinusoidal sigma weight residual 0.00 89.96 -89.96 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 474 " pdb=" CG GLU A 474 " pdb=" CD GLU A 474 " pdb=" OE1 GLU A 474 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 470 " pdb=" CD ARG B 470 " pdb=" NE ARG B 470 " pdb=" CZ ARG B 470 " ideal model delta sinusoidal sigma weight residual 90.00 134.84 -44.84 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 649 0.042 - 0.083: 176 0.083 - 0.125: 44 0.125 - 0.166: 1 0.166 - 0.208: 1 Chirality restraints: 871 Sorted by residual: chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 250 " pdb=" N ILE B 250 " pdb=" C ILE B 250 " pdb=" CB ILE B 250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL B 451 " pdb=" N VAL B 451 " pdb=" C VAL B 451 " pdb=" CB VAL B 451 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 868 not shown) Planarity restraints: 989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 191 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO A 192 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 247 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 248 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 248 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 248 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 191 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO B 192 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.027 5.00e-02 4.00e+02 ... (remaining 986 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1075 2.78 - 3.31: 4948 3.31 - 3.84: 8256 3.84 - 4.37: 10490 4.37 - 4.90: 18138 Nonbonded interactions: 42907 Sorted by model distance: nonbonded pdb=" OH TYR B 439 " pdb=" O LEU B 463 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 201 " pdb=" OD1 ASN A 231 " model vdw 2.261 3.040 nonbonded pdb=" O TYR B 215 " pdb=" NH1 ARG B 241 " model vdw 2.272 3.120 nonbonded pdb=" OE2 GLU A 323 " pdb=" NH2 ARG A 549 " model vdw 2.280 3.120 nonbonded pdb=" OH TYR B 201 " pdb=" OE1 GLU B 234 " model vdw 2.287 3.040 ... (remaining 42902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 189 through 239 or resid 241 through 518 or resid 532 thro \ ugh 559 or resid 561 through 567)) selection = (chain 'B' and (resid 173 or resid 190 through 239 or resid 241 through 518 or r \ esid 532 through 559 or resid 561 through 567)) } 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=0.50 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.002 0.032 5725 Z= 0.102 Angle : 0.496 7.559 7783 Z= 0.247 Chirality : 0.039 0.208 871 Planarity : 0.005 0.073 989 Dihedral : 14.042 89.963 2127 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.75 (0.31), residues: 686 helix: -1.43 (0.28), residues: 280 sheet: -0.36 (0.57), residues: 97 loop : -0.99 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 549 TYR 0.010 0.001 TYR A 201 PHE 0.013 0.001 PHE A 401 TRP 0.005 0.001 TRP B 533 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 5725) covalent geometry : angle 0.49561 / 0.25 ( 7783) hydrogen bonds : bond 0.30111 / 19.47 ( 230) hydrogen bonds : angle 7.93293 / 5.43 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0905 time to fit residues: 7.5236 Evaluate side-chains 55 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 ASN ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.204157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159036 restraints weight = 13860.787| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.72 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5725 Z= 0.114 Angle : 0.531 5.735 7783 Z= 0.272 Chirality : 0.041 0.180 871 Planarity : 0.005 0.071 989 Dihedral : 3.740 16.060 758 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.32 % Allowed : 4.52 % Favored : 95.15 % 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: -0.28 (0.33), residues: 686 helix: 0.61 (0.31), residues: 283 sheet: -0.18 (0.58), residues: 93 loop : -0.87 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 465 TYR 0.010 0.001 TYR A 201 PHE 0.010 0.001 PHE A 401 TRP 0.010 0.001 TRP A 412 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 5725) covalent geometry : angle 0.53141 / 0.27 ( 7783) hydrogen bonds : bond 0.05022 / 3.29 ( 230) hydrogen bonds : angle 4.88352 / 3.33 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.140 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0876 time to fit residues: 7.2131 Evaluate side-chains 61 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [38, 37, 51, 66, 6, 58, 31, 50, 33, 39, 15] chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.201278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162754 restraints weight = 14458.971| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.22 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5725 Z= 0.146 Angle : 0.548 5.591 7783 Z= 0.271 Chirality : 0.042 0.140 871 Planarity : 0.005 0.069 989 Dihedral : 3.879 15.560 758 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.65 % Allowed : 7.27 % Favored : 92.08 % 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: 0.03 (0.33), residues: 686 helix: 1.19 (0.33), residues: 285 sheet: -0.14 (0.58), residues: 91 loop : -1.03 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.012 0.001 TYR A 201 PHE 0.015 0.002 PHE A 291 TRP 0.007 0.001 TRP B 412 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 5725) covalent geometry : angle 0.54818 / 0.27 ( 7783) hydrogen bonds : bond 0.05099 / 3.33 ( 230) hydrogen bonds : angle 4.58384 / 3.13 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.198 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.0974 time to fit residues: 7.8344 Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [6, 52, 26, 31, 30, 0, 9, 12, 27, 56, 47] chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152564 restraints weight = 12363.312| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 6.21 r_work: 0.3374 rms_B_bonded: 6.04 restraints_weight: 2.0000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5725 Z= 0.122 Angle : 0.515 5.639 7783 Z= 0.257 Chirality : 0.041 0.135 871 Planarity : 0.005 0.064 989 Dihedral : 3.824 14.988 758 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.65 % Allowed : 9.21 % Favored : 90.15 % 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: 0.14 (0.33), residues: 686 helix: 1.40 (0.33), residues: 285 sheet: -0.23 (0.57), residues: 91 loop : -1.05 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.011 0.001 TYR A 201 PHE 0.014 0.001 PHE A 291 TRP 0.008 0.001 TRP A 412 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 5725) covalent geometry : angle 0.51478 / 0.26 ( 7783) hydrogen bonds : bond 0.04077 / 2.67 ( 230) hydrogen bonds : angle 4.32120 / 2.94 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.138 Fit side-chains REVERT: B 196 LYS cc_start: 0.6623 (tttt) cc_final: 0.6408 (tttp) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.0944 time to fit residues: 8.0638 Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [36, 7, 53, 42, 26, 55, 33, 21, 59, 31, 40] chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS A 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.201793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155022 restraints weight = 7971.169| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.91 r_work: 0.3487 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5725 Z= 0.124 Angle : 0.516 6.104 7783 Z= 0.256 Chirality : 0.041 0.135 871 Planarity : 0.005 0.059 989 Dihedral : 3.823 14.450 758 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.97 % Allowed : 10.18 % Favored : 88.85 % 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: 0.18 (0.33), residues: 686 helix: 1.47 (0.34), residues: 285 sheet: -0.31 (0.56), residues: 92 loop : -1.03 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.011 0.001 TYR A 201 PHE 0.014 0.001 PHE A 291 TRP 0.007 0.001 TRP A 412 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.12 ( 5725) covalent geometry : angle 0.51636 / 0.26 ( 7783) hydrogen bonds : bond 0.04036 / 2.63 ( 230) hydrogen bonds : angle 4.19381 / 2.85 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.159 Fit side-chains REVERT: B 196 LYS cc_start: 0.6578 (tttt) cc_final: 0.6378 (tttp) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.0835 time to fit residues: 7.2832 Evaluate side-chains 71 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [65, 16, 40, 60, 29, 64, 32, 21, 28, 33, 58] chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 overall best weight: 0.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.203646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.157081 restraints weight = 14413.475| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 6.15 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5725 Z= 0.097 Angle : 0.476 5.876 7783 Z= 0.239 Chirality : 0.040 0.130 871 Planarity : 0.005 0.057 989 Dihedral : 3.683 13.935 758 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.81 % Allowed : 10.66 % Favored : 88.53 % 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: 0.35 (0.34), residues: 686 helix: 1.67 (0.34), residues: 285 sheet: -0.38 (0.56), residues: 94 loop : -0.94 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.010 0.001 TYR A 201 PHE 0.013 0.001 PHE A 291 TRP 0.009 0.001 TRP A 412 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 5725) covalent geometry : angle 0.47607 / 0.24 ( 7783) hydrogen bonds : bond 0.03273 / 2.14 ( 230) hydrogen bonds : angle 4.01708 / 2.72 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.242 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.0815 time to fit residues: 6.6704 Evaluate side-chains 66 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [23, 27, 47, 12, 39, 52, 10, 4, 25, 53, 7] chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 7 optimal weight: 0.5980 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.204427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161849 restraints weight = 15841.842| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 5.14 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5725 Z= 0.097 Angle : 0.475 6.140 7783 Z= 0.237 Chirality : 0.040 0.130 871 Planarity : 0.005 0.054 989 Dihedral : 3.622 13.912 758 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.97 % Allowed : 10.34 % Favored : 88.69 % 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: 0.49 (0.34), residues: 686 helix: 1.81 (0.34), residues: 285 sheet: -0.18 (0.57), residues: 92 loop : -0.93 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.009 0.001 TYR A 201 PHE 0.013 0.001 PHE A 291 TRP 0.008 0.001 TRP A 412 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 5725) covalent geometry : angle 0.47458 / 0.24 ( 7783) hydrogen bonds : bond 0.03238 / 2.11 ( 230) hydrogen bonds : angle 3.92743 / 2.66 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.198 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.0849 time to fit residues: 6.9966 Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 377 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [4, 32, 46, 20, 21, 34, 22, 37, 3, 48, 30] chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.204284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149622 restraints weight = 12674.242| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 7.80 r_work: 0.3398 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5725 Z= 0.110 Angle : 0.492 6.094 7783 Z= 0.244 Chirality : 0.040 0.132 871 Planarity : 0.005 0.054 989 Dihedral : 3.690 13.896 758 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.97 % Allowed : 10.34 % Favored : 88.69 % 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: 0.49 (0.34), residues: 686 helix: 1.80 (0.33), residues: 285 sheet: -0.25 (0.57), residues: 93 loop : -0.90 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.009 0.001 TYR A 201 PHE 0.014 0.001 PHE A 291 TRP 0.007 0.001 TRP A 412 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 5725) covalent geometry : angle 0.49192 / 0.24 ( 7783) hydrogen bonds : bond 0.03530 / 2.29 ( 230) hydrogen bonds : angle 3.92323 / 2.65 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.201 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.0848 time to fit residues: 7.1596 Evaluate side-chains 66 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [45, 66, 48, 23, 4, 21, 12, 28, 36, 54, 61] chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.200110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152378 restraints weight = 12405.187| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 5.83 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5725 Z= 0.163 Angle : 0.566 6.735 7783 Z= 0.277 Chirality : 0.043 0.138 871 Planarity : 0.005 0.052 989 Dihedral : 3.944 14.225 758 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.37 % 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: 0.22 (0.33), residues: 686 helix: 1.51 (0.33), residues: 285 sheet: -0.15 (0.57), residues: 91 loop : -1.06 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.012 0.001 TYR A 201 PHE 0.017 0.002 PHE A 291 TRP 0.008 0.001 TRP A 533 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.16 ( 5725) covalent geometry : angle 0.56598 / 0.28 ( 7783) hydrogen bonds : bond 0.04581 / 2.96 ( 230) hydrogen bonds : angle 4.07818 / 2.76 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.222 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.0810 time to fit residues: 6.8213 Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [17, 19, 44, 4, 12, 26, 36, 1, 18, 58, 11] chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.0060 chunk 11 optimal weight: 0.2980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.203798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158229 restraints weight = 6933.616| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.28 r_work: 0.3504 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5725 Z= 0.098 Angle : 0.479 5.965 7783 Z= 0.240 Chirality : 0.040 0.130 871 Planarity : 0.005 0.052 989 Dihedral : 3.722 13.502 758 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.37 % 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: 0.50 (0.34), residues: 686 helix: 1.81 (0.34), residues: 286 sheet: -0.25 (0.57), residues: 93 loop : -0.90 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.009 0.001 TYR A 201 PHE 0.013 0.001 PHE A 291 TRP 0.009 0.001 TRP A 412 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 5725) covalent geometry : angle 0.47869 / 0.24 ( 7783) hydrogen bonds : bond 0.03244 / 2.10 ( 230) hydrogen bonds : angle 3.90732 / 2.64 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.204 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.0871 time to fit residues: 7.5016 Evaluate side-chains 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [53, 1, 26, 29, 50, 11, 16, 58, 8, 7, 0] chunk 53 optimal weight: 0.0370 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.205995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154520 restraints weight = 11595.870| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 6.30 r_work: 0.3493 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5725 Z= 0.080 Angle : 0.446 5.848 7783 Z= 0.226 Chirality : 0.039 0.125 871 Planarity : 0.005 0.051 989 Dihedral : 3.489 13.625 758 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.48 % Allowed : 10.99 % Favored : 88.53 % 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: 0.79 (0.34), residues: 686 helix: 2.07 (0.34), residues: 287 sheet: -0.12 (0.57), residues: 92 loop : -0.76 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.009 0.001 TYR A 201 PHE 0.011 0.001 PHE A 291 TRP 0.010 0.001 TRP A 412 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 ( 5725) covalent geometry : angle 0.44639 / 0.23 ( 7783) hydrogen bonds : bond 0.02493 / 1.62 ( 230) hydrogen bonds : angle 3.76745 / 2.55 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.59 seconds wall clock time: 25 minutes 50.13 seconds (1550.13 seconds total)