Starting phenix.real_space_refine on Thu Jul 2 02:42:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2026/9kmj_62435.map" } resolution = 3.1 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3953 2.51 5 N 950 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4282 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 27, 'TRANS': 508} Chain breaks: 1 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 8 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1, 'water': 1} Chain breaks: 3 Time building chain proxies: 1.33, per 1000 atoms: 0.22 Number of scatterers: 6019 At special positions: 0 Unit cell: (77.08, 82.82, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 43 16.00 Na 2 11.00 O 1070 8.00 N 950 7.00 C 3953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.33 Conformation dependent library (CDL) restraints added in 128.9 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 55.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.024A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.614A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.699A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.605A pdb=" N LYS A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 116 " --> pdb=" O TRP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.733A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 247 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.586A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.558A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.362A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.572A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.593A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.619A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.906A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.804A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.529A pdb=" N TYR A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.617A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.928A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.552A pdb=" N TYR A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.125A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.927A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.895A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.540A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 963 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: 0.97 Time building geometry restraints manager: 0.45 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: 1761 1.34 - 1.46: 1514 1.46 - 1.58: 2855 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6193 Sorted by residual: bond pdb=" CB PRO A 68 " pdb=" CG PRO A 68 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CD GLU A 406 " pdb=" OE1 GLU A 406 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.32e+00 bond pdb=" C TYR L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.334 1.368 -0.035 2.34e-02 1.83e+03 2.18e+00 bond pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 6188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8112 2.02 - 4.04: 257 4.04 - 6.06: 33 6.06 - 8.08: 11 8.08 - 10.10: 9 Bond angle restraints: 8422 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" CA PRO A 208 " pdb=" N PRO A 208 " pdb=" CD PRO A 208 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" C GLY A 425 " pdb=" N TYR A 426 " pdb=" CA TYR A 426 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C PRO A 68 " pdb=" N TYR A 69 " pdb=" CA TYR A 69 " ideal model delta sigma weight residual 121.14 114.89 6.25 1.75e+00 3.27e-01 1.27e+01 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 121.14 114.90 6.24 1.75e+00 3.27e-01 1.27e+01 ... (remaining 8417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3173 16.96 - 33.92: 306 33.92 - 50.88: 60 50.88 - 67.84: 4 67.84 - 84.79: 5 Dihedral angle restraints: 3548 sinusoidal: 1358 harmonic: 2190 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N TYR A 302 " pdb=" CA TYR A 302 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 654 0.048 - 0.096: 196 0.096 - 0.143: 52 0.143 - 0.191: 14 0.191 - 0.239: 4 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 261 " pdb=" CB LEU A 261 " pdb=" CD1 LEU A 261 " pdb=" CD2 LEU A 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 917 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.045 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 208 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 402 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C SER A 402 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 402 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 403 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 253 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.036 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1422 2.78 - 3.31: 5637 3.31 - 3.84: 10901 3.84 - 4.37: 12917 4.37 - 4.90: 22504 Nonbonded interactions: 53381 Sorted by model distance: nonbonded pdb=" OD1 ASP A 494 " pdb=" OH TYR H 59 " model vdw 2.251 3.040 nonbonded pdb=" NE ARG A 493 " pdb=" O GLU H 100 " model vdw 2.332 3.120 nonbonded pdb=" O ALA A 343 " pdb=" OG SER A 346 " model vdw 2.334 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.357 3.120 nonbonded pdb=" O ASN L 2 " pdb=" OG1 THR L 98 " model vdw 2.362 3.040 ... (remaining 53376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.006 0.082 6196 Z= 0.253 Angle : 0.877 10.105 8428 Z= 0.465 Chirality : 0.052 0.239 920 Planarity : 0.007 0.065 1036 Dihedral : 13.752 84.794 2153 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.43 (0.29), residues: 754 helix: -0.67 (0.24), residues: 364 sheet: -1.15 (0.52), residues: 103 loop : -0.99 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 62 TYR 0.026 0.002 TYR A 137 PHE 0.042 0.003 PHE A 338 TRP 0.031 0.002 TRP A 44 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.25 ( 6193) covalent geometry : angle 0.87585 / 0.46 ( 8422) SS BOND : bond 0.00372 / 0.26 ( 3) SS BOND : angle 1.60857 / 1.20 ( 6) hydrogen bonds : bond 0.16404 / 11.04 ( 329) hydrogen bonds : angle 7.43160 / 5.08 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.216 Fit side-chains REVERT: H 32 TYR cc_start: 0.7454 (m-80) cc_final: 0.7181 (m-80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0584 time to fit residues: 8.1855 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135561 restraints weight = 6602.428| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.98 r_work: 0.3353 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6196 Z= 0.173 Angle : 0.613 7.633 8428 Z= 0.320 Chirality : 0.041 0.153 920 Planarity : 0.005 0.052 1036 Dihedral : 5.206 40.192 835 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.30), residues: 754 helix: 0.38 (0.26), residues: 366 sheet: -0.83 (0.52), residues: 98 loop : -0.77 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.022 0.002 PHE A 338 TRP 0.019 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 6193) covalent geometry : angle 0.61245 / 0.32 ( 8422) SS BOND : bond 0.00212 / 0.10 ( 3) SS BOND : angle 0.97775 / 0.69 ( 6) hydrogen bonds : bond 0.04868 / 3.05 ( 329) hydrogen bonds : angle 5.48284 / 3.69 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.211 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.0647 time to fit residues: 8.9152 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145431 restraints weight = 6449.429| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.91 r_work: 0.3541 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6196 Z= 0.113 Angle : 0.533 7.495 8428 Z= 0.276 Chirality : 0.039 0.148 920 Planarity : 0.005 0.048 1036 Dihedral : 4.852 53.319 835 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.46 % Allowed : 8.63 % Favored : 90.91 % 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: 0.31 (0.31), residues: 754 helix: 1.13 (0.27), residues: 361 sheet: -0.41 (0.53), residues: 98 loop : -0.65 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 493 TYR 0.022 0.001 TYR A 137 PHE 0.017 0.001 PHE A 350 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6193) covalent geometry : angle 0.53316 / 0.28 ( 8422) SS BOND : bond 0.00235 / 0.13 ( 3) SS BOND : angle 0.85862 / 0.60 ( 6) hydrogen bonds : bond 0.04102 / 2.54 ( 329) hydrogen bonds : angle 4.85269 / 3.26 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.214 Fit side-chains REVERT: H 56 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.8196 (mtm-85) outliers start: 3 outliers final: 3 residues processed: 105 average time/residue: 0.0687 time to fit residues: 9.7373 Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 61 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.171929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137989 restraints weight = 6609.248| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.98 r_work: 0.3464 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6196 Z= 0.132 Angle : 0.540 7.452 8428 Z= 0.280 Chirality : 0.040 0.149 920 Planarity : 0.005 0.062 1036 Dihedral : 4.786 56.169 835 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.62 % Allowed : 11.40 % Favored : 87.98 % 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: 0.58 (0.31), residues: 754 helix: 1.37 (0.27), residues: 362 sheet: -0.22 (0.53), residues: 98 loop : -0.58 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.019 0.002 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6193) covalent geometry : angle 0.53965 / 0.28 ( 8422) SS BOND : bond 0.00225 / 0.11 ( 3) SS BOND : angle 0.65135 / 0.39 ( 6) hydrogen bonds : bond 0.04184 / 2.62 ( 329) hydrogen bonds : angle 4.75058 / 3.19 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.154 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 0.0701 time to fit residues: 9.4332 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131923 restraints weight = 6701.299| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.96 r_work: 0.3435 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.171 Angle : 0.563 7.675 8428 Z= 0.293 Chirality : 0.041 0.150 920 Planarity : 0.005 0.062 1036 Dihedral : 4.857 58.146 835 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.23 % Allowed : 12.02 % Favored : 86.75 % 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: 0.62 (0.31), residues: 754 helix: 1.33 (0.28), residues: 362 sheet: -0.05 (0.52), residues: 103 loop : -0.51 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.025 0.002 PHE A 434 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6193) covalent geometry : angle 0.56316 / 0.29 ( 8422) SS BOND : bond 0.00252 / 0.14 ( 3) SS BOND : angle 0.61050 / 0.34 ( 6) hydrogen bonds : bond 0.04487 / 2.82 ( 329) hydrogen bonds : angle 4.84699 / 3.26 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.6833 (p90) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.0620 time to fit residues: 8.7938 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131229 restraints weight = 6718.902| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.92 r_work: 0.3192 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 6196 Z= 0.301 Angle : 0.666 7.965 8428 Z= 0.347 Chirality : 0.045 0.154 920 Planarity : 0.005 0.065 1036 Dihedral : 5.164 58.429 835 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.23 % Allowed : 13.25 % Favored : 85.52 % 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: 0.26 (0.31), residues: 754 helix: 1.02 (0.28), residues: 362 sheet: -0.53 (0.49), residues: 111 loop : -0.52 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 66 TYR 0.023 0.002 TYR A 137 PHE 0.032 0.003 PHE A 404 TRP 0.018 0.002 TRP A 470 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.30 ( 6193) covalent geometry : angle 0.66605 / 0.35 ( 8422) SS BOND : bond 0.00351 / 0.21 ( 3) SS BOND : angle 0.76979 / 0.41 ( 6) hydrogen bonds : bond 0.05319 / 3.37 ( 329) hydrogen bonds : angle 5.27784 / 3.56 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.253 Fit side-chains REVERT: A 69 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.6873 (p90) REVERT: A 401 ASP cc_start: 0.7584 (m-30) cc_final: 0.7351 (m-30) REVERT: H 30 SER cc_start: 0.9105 (m) cc_final: 0.8864 (p) REVERT: H 90 ASP cc_start: 0.8684 (t0) cc_final: 0.8162 (t0) REVERT: L 91 GLN cc_start: 0.9128 (pp30) cc_final: 0.8424 (pp30) outliers start: 8 outliers final: 7 residues processed: 104 average time/residue: 0.0757 time to fit residues: 10.5491 Evaluate side-chains 103 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 49 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136673 restraints weight = 6639.868| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.90 r_work: 0.3440 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6196 Z= 0.163 Angle : 0.571 7.990 8428 Z= 0.296 Chirality : 0.041 0.151 920 Planarity : 0.005 0.058 1036 Dihedral : 4.974 58.055 835 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.23 % Allowed : 13.25 % Favored : 85.52 % 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: 0.51 (0.31), residues: 754 helix: 1.19 (0.27), residues: 363 sheet: -0.37 (0.48), residues: 108 loop : -0.36 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.030 0.002 PHE A 404 TRP 0.018 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 6193) covalent geometry : angle 0.57074 / 0.30 ( 8422) SS BOND : bond 0.00229 / 0.11 ( 3) SS BOND : angle 0.52912 / 0.27 ( 6) hydrogen bonds : bond 0.04497 / 2.84 ( 329) hydrogen bonds : angle 4.99799 / 3.37 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.145 Fit side-chains REVERT: A 69 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.6577 (p90) REVERT: L 91 GLN cc_start: 0.9103 (pp30) cc_final: 0.8455 (pp30) outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 0.0725 time to fit residues: 9.9100 Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135420 restraints weight = 6684.313| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.90 r_work: 0.3310 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6196 Z= 0.191 Angle : 0.597 7.971 8428 Z= 0.307 Chirality : 0.042 0.154 920 Planarity : 0.005 0.059 1036 Dihedral : 5.000 59.400 835 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.08 % Allowed : 13.25 % Favored : 85.67 % 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: 0.56 (0.32), residues: 754 helix: 1.24 (0.27), residues: 363 sheet: -0.32 (0.50), residues: 103 loop : -0.37 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.033 0.002 PHE A 404 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 6193) covalent geometry : angle 0.59662 / 0.31 ( 8422) SS BOND : bond 0.00232 / 0.11 ( 3) SS BOND : angle 0.51105 / 0.25 ( 6) hydrogen bonds : bond 0.04614 / 2.92 ( 329) hydrogen bonds : angle 5.01516 / 3.37 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.192 Fit side-chains REVERT: A 69 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.6832 (p90) REVERT: L 91 GLN cc_start: 0.9112 (pp30) cc_final: 0.8420 (pp30) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.0683 time to fit residues: 9.0506 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134652 restraints weight = 6737.303| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.98 r_work: 0.3396 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6196 Z= 0.151 Angle : 0.572 8.201 8428 Z= 0.295 Chirality : 0.041 0.151 920 Planarity : 0.005 0.053 1036 Dihedral : 4.911 58.892 835 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.39 % Allowed : 12.79 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.67 (0.32), residues: 754 helix: 1.35 (0.27), residues: 363 sheet: -0.21 (0.50), residues: 103 loop : -0.37 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.035 0.002 PHE A 404 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6193) covalent geometry : angle 0.57175 / 0.29 ( 8422) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 0.46821 / 0.25 ( 6) hydrogen bonds : bond 0.04337 / 2.74 ( 329) hydrogen bonds : angle 4.89577 / 3.28 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.220 Fit side-chains REVERT: A 69 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.6594 (p90) REVERT: L 91 GLN cc_start: 0.9115 (pp30) cc_final: 0.8332 (pp30) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 0.0740 time to fit residues: 9.6428 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 0.0370 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136656 restraints weight = 6665.586| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.96 r_work: 0.3452 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6196 Z= 0.142 Angle : 0.567 8.253 8428 Z= 0.291 Chirality : 0.041 0.153 920 Planarity : 0.005 0.048 1036 Dihedral : 4.821 57.770 835 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.54 % Allowed : 12.94 % Favored : 85.52 % 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 (0.32), residues: 754 helix: 1.47 (0.28), residues: 362 sheet: -0.19 (0.50), residues: 104 loop : -0.32 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.035 0.002 PHE A 404 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6193) covalent geometry : angle 0.56718 / 0.29 ( 8422) SS BOND : bond 0.00227 / 0.12 ( 3) SS BOND : angle 0.46851 / 0.26 ( 6) hydrogen bonds : bond 0.04222 / 2.67 ( 329) hydrogen bonds : angle 4.80108 / 3.22 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.6612 (p90) REVERT: L 17 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7824 (tm-30) REVERT: L 91 GLN cc_start: 0.9100 (pp30) cc_final: 0.8349 (pp30) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.0693 time to fit residues: 9.4674 Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144776 restraints weight = 6601.514| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.94 r_work: 0.3296 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6196 Z= 0.128 Angle : 0.554 8.349 8428 Z= 0.284 Chirality : 0.040 0.153 920 Planarity : 0.005 0.048 1036 Dihedral : 4.743 57.962 835 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.23 % Allowed : 13.71 % Favored : 85.05 % 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: 0.91 (0.32), residues: 754 helix: 1.59 (0.28), residues: 362 sheet: -0.12 (0.51), residues: 104 loop : -0.32 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.033 0.002 PHE A 404 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6193) covalent geometry : angle 0.55452 / 0.28 ( 8422) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 0.47963 / 0.29 ( 6) hydrogen bonds : bond 0.04114 / 2.60 ( 329) hydrogen bonds : angle 4.68431 / 3.13 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.96 seconds wall clock time: 29 minutes 57.37 seconds (1797.37 seconds total)