Starting phenix.real_space_refine on Thu Jul 2 02:23:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.map" model { file = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kml_62437/07_2026/9kml_62437.cif" } resolution = 3.11 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= 0.021 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 Cl 1 4.86 5 C 3854 2.51 5 N 931 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 5872 Number of models: 1 Model: "" Number of chains: 4 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: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4145 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 1 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.17 Number of scatterers: 5872 At special positions: 0 Unit cell: (72.16, 82.82, 113.16, 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) Cl 1 17.00 S 41 16.00 O 1045 8.00 N 931 7.00 C 3854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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: 0.31 Conformation dependent library (CDL) restraints added in 220.6 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 54.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.587A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.852A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.873A 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 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.772A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 4.184A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 219 through 236 removed outlier: 4.328A pdb=" N TRP A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 removed outlier: 3.739A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 4.170A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.551A pdb=" N GLY A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.293A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.574A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 356 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.653A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.666A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.939A 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 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.612A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.835A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.940A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.566A pdb=" N SER H 71 " --> pdb=" O HIS H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.859A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.859A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 12.362A pdb=" N CYS L 23 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N THR L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA L 25 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N SER L 73 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N SER L 27 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER L 71 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L 69 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.469A 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: 5.793A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 915 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: 0.99 Time building geometry restraints manager: 0.46 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: 1741 1.34 - 1.46: 1385 1.46 - 1.58: 2855 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6041 Sorted by residual: bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.496 0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" CB VAL A 140 " pdb=" CG1 VAL A 140 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.65e+00 bond pdb=" C THR A 512 " pdb=" N PRO A 513 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.41e+00 bond pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " ideal model delta sigma weight residual 1.526 1.501 0.026 1.76e-02 3.23e+03 2.10e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7948 2.23 - 4.46: 228 4.46 - 6.69: 28 6.69 - 8.92: 8 8.92 - 11.15: 1 Bond angle restraints: 8213 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 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C TRP A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 121.97 129.62 -7.65 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 121.14 114.51 6.63 1.75e+00 3.27e-01 1.43e+01 angle pdb=" C ILE A 139 " pdb=" N VAL A 140 " pdb=" CA VAL A 140 " ideal model delta sigma weight residual 120.64 115.00 5.64 1.64e+00 3.72e-01 1.18e+01 ... (remaining 8208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3096 17.21 - 34.42: 304 34.42 - 51.63: 49 51.63 - 68.84: 8 68.84 - 86.05: 6 Dihedral angle restraints: 3463 sinusoidal: 1323 harmonic: 2140 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -167.10 81.10 1 1.00e+01 1.00e-02 8.12e+01 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 51.16 41.84 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA HIS A 161 " pdb=" C HIS A 161 " pdb=" N CYS A 162 " pdb=" CA CYS A 162 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 3460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 603 0.045 - 0.090: 210 0.090 - 0.135: 69 0.135 - 0.180: 12 0.180 - 0.224: 5 Chirality restraints: 899 Sorted by residual: chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+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 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 140 " pdb=" CA VAL A 140 " pdb=" CG1 VAL A 140 " pdb=" CG2 VAL A 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 896 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO A 93 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 219 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ASP A 219 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 219 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 220 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 479 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ILE A 479 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 479 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 480 " -0.015 2.00e-02 2.50e+03 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1119 2.77 - 3.30: 5491 3.30 - 3.83: 10597 3.83 - 4.37: 12248 4.37 - 4.90: 21481 Nonbonded interactions: 50936 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.235 3.040 nonbonded pdb=" O LYS A 376 " pdb=" OG1 THR A 379 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASP A 174 " pdb=" OG SER A 193 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR A 72 " pdb=" O ILE A 359 " model vdw 2.359 3.040 nonbonded pdb=" NH1 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 2.364 3.120 ... (remaining 50931 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: 5.550 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.062 6044 Z= 0.253 Angle : 0.884 11.151 8219 Z= 0.488 Chirality : 0.053 0.224 899 Planarity : 0.008 0.082 1013 Dihedral : 13.751 86.049 2102 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % 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: -1.86 (0.28), residues: 738 helix: -0.90 (0.24), residues: 352 sheet: -1.22 (0.51), residues: 108 loop : -1.46 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 201 TYR 0.029 0.002 TYR H 57 PHE 0.031 0.003 PHE L 92 TRP 0.015 0.002 TRP A 65 HIS 0.006 0.002 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 6041) covalent geometry : angle 0.88356 / 0.49 ( 8213) SS BOND : bond 0.00189 / 0.09 ( 3) SS BOND : angle 1.22339 / 0.68 ( 6) hydrogen bonds : bond 0.15836 / 10.84 ( 316) hydrogen bonds : angle 7.35374 / 5.02 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.149 Fit side-chains REVERT: H 57 TYR cc_start: 0.8511 (m-80) cc_final: 0.7904 (m-80) REVERT: A 72 TYR cc_start: 0.8511 (t80) cc_final: 0.8076 (t80) REVERT: A 191 PHE cc_start: 0.7389 (m-80) cc_final: 0.7168 (m-80) REVERT: A 258 LEU cc_start: 0.7975 (tp) cc_final: 0.7732 (mt) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.0747 time to fit residues: 11.8718 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.160258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131884 restraints weight = 7042.466| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.85 r_work: 0.3297 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6044 Z= 0.208 Angle : 0.624 8.275 8219 Z= 0.334 Chirality : 0.043 0.158 899 Planarity : 0.006 0.070 1013 Dihedral : 5.050 19.939 819 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.74 % Allowed : 9.02 % Favored : 89.24 % 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: -0.97 (0.30), residues: 738 helix: 0.18 (0.26), residues: 359 sheet: -1.56 (0.48), residues: 117 loop : -1.18 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 240 TYR 0.018 0.002 TYR A 137 PHE 0.020 0.002 PHE A 455 TRP 0.028 0.002 TRP A 218 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 6041) covalent geometry : angle 0.62384 / 0.33 ( 8213) SS BOND : bond 0.00272 / 0.13 ( 3) SS BOND : angle 0.87427 / 0.49 ( 6) hydrogen bonds : bond 0.04851 / 3.29 ( 316) hydrogen bonds : angle 5.47452 / 3.66 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.210 Fit side-chains REVERT: H 46 GLU cc_start: 0.8773 (tt0) cc_final: 0.8341 (tt0) REVERT: H 57 TYR cc_start: 0.8926 (m-80) cc_final: 0.8455 (m-80) REVERT: H 78 ILE cc_start: 0.8102 (mp) cc_final: 0.7828 (mp) REVERT: A 191 PHE cc_start: 0.7625 (m-80) cc_final: 0.7246 (m-80) REVERT: A 440 TYR cc_start: 0.8215 (t80) cc_final: 0.7980 (t80) outliers start: 11 outliers final: 8 residues processed: 111 average time/residue: 0.0758 time to fit residues: 11.0475 Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130220 restraints weight = 6907.865| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.89 r_work: 0.3326 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6044 Z= 0.158 Angle : 0.567 7.191 8219 Z= 0.302 Chirality : 0.042 0.167 899 Planarity : 0.005 0.064 1013 Dihedral : 4.741 18.297 819 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 12.18 % Favored : 85.92 % 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: -0.46 (0.31), residues: 738 helix: 0.71 (0.26), residues: 359 sheet: -1.41 (0.49), residues: 112 loop : -1.07 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.022 0.001 TYR A 137 PHE 0.018 0.002 PHE A 473 TRP 0.020 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6041) covalent geometry : angle 0.56648 / 0.30 ( 8213) SS BOND : bond 0.00165 / 0.08 ( 3) SS BOND : angle 0.60923 / 0.34 ( 6) hydrogen bonds : bond 0.04467 / 3.05 ( 316) hydrogen bonds : angle 5.17091 / 3.45 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.147 Fit side-chains REVERT: H 46 GLU cc_start: 0.8833 (tt0) cc_final: 0.8316 (tt0) REVERT: H 57 TYR cc_start: 0.8949 (m-80) cc_final: 0.8416 (m-80) REVERT: H 78 ILE cc_start: 0.7918 (mp) cc_final: 0.7615 (mp) REVERT: A 191 PHE cc_start: 0.7639 (m-80) cc_final: 0.7280 (m-80) REVERT: A 218 TRP cc_start: 0.6231 (t60) cc_final: 0.5453 (p-90) REVERT: A 440 TYR cc_start: 0.8465 (t80) cc_final: 0.8085 (t80) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.0690 time to fit residues: 10.5464 Evaluate side-chains 114 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.156860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126137 restraints weight = 6965.482| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.13 r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6044 Z= 0.186 Angle : 0.583 8.810 8219 Z= 0.310 Chirality : 0.042 0.172 899 Planarity : 0.005 0.063 1013 Dihedral : 4.673 18.331 819 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.85 % Allowed : 13.61 % Favored : 83.54 % 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: -0.23 (0.31), residues: 738 helix: 0.84 (0.26), residues: 360 sheet: -1.20 (0.51), residues: 105 loop : -0.94 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.021 0.002 TYR A 137 PHE 0.019 0.002 PHE A 455 TRP 0.019 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 6041) covalent geometry : angle 0.58319 / 0.31 ( 8213) SS BOND : bond 0.00188 / 0.09 ( 3) SS BOND : angle 0.57003 / 0.31 ( 6) hydrogen bonds : bond 0.04543 / 3.11 ( 316) hydrogen bonds : angle 5.12843 / 3.42 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.143 Fit side-chains REVERT: H 46 GLU cc_start: 0.8880 (tt0) cc_final: 0.8319 (tt0) REVERT: H 57 TYR cc_start: 0.8977 (m-80) cc_final: 0.8462 (m-80) REVERT: H 78 ILE cc_start: 0.7902 (mp) cc_final: 0.7573 (mp) REVERT: A 191 PHE cc_start: 0.7694 (m-80) cc_final: 0.7293 (m-80) REVERT: A 225 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7817 (tt) REVERT: A 440 TYR cc_start: 0.8585 (t80) cc_final: 0.8112 (t80) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.0761 time to fit residues: 11.0598 Evaluate side-chains 115 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.156240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127430 restraints weight = 7103.703| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.95 r_work: 0.3307 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6044 Z= 0.167 Angle : 0.564 8.556 8219 Z= 0.299 Chirality : 0.041 0.172 899 Planarity : 0.005 0.060 1013 Dihedral : 4.590 18.219 819 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.80 % Allowed : 13.92 % Favored : 82.28 % 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 (0.31), residues: 738 helix: 0.98 (0.27), residues: 360 sheet: -1.38 (0.49), residues: 112 loop : -0.87 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 62 TYR 0.022 0.001 TYR A 137 PHE 0.013 0.002 PHE A 455 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 6041) covalent geometry : angle 0.56408 / 0.30 ( 8213) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 0.84234 / 0.39 ( 6) hydrogen bonds : bond 0.04334 / 2.98 ( 316) hydrogen bonds : angle 5.02999 / 3.36 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.221 Fit side-chains REVERT: H 46 GLU cc_start: 0.8878 (tt0) cc_final: 0.8341 (tt0) REVERT: H 57 TYR cc_start: 0.8988 (m-80) cc_final: 0.8515 (m-80) REVERT: H 78 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 155 LYS cc_start: 0.8479 (tttp) cc_final: 0.7418 (mmtt) REVERT: A 191 PHE cc_start: 0.7734 (m-80) cc_final: 0.7312 (m-80) REVERT: A 225 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7884 (tt) outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 0.0755 time to fit residues: 11.7299 Evaluate side-chains 121 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.159169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128885 restraints weight = 6914.534| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.12 r_work: 0.3344 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6044 Z= 0.134 Angle : 0.539 7.938 8219 Z= 0.286 Chirality : 0.041 0.174 899 Planarity : 0.005 0.057 1013 Dihedral : 4.423 16.849 819 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 15.19 % Favored : 81.65 % 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: 0.09 (0.32), residues: 738 helix: 1.18 (0.27), residues: 359 sheet: -1.25 (0.50), residues: 112 loop : -0.79 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.023 0.001 TYR A 137 PHE 0.011 0.001 PHE A 455 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6041) covalent geometry : angle 0.53911 / 0.29 ( 8213) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 0.72013 / 0.34 ( 6) hydrogen bonds : bond 0.04054 / 2.80 ( 316) hydrogen bonds : angle 4.88704 / 3.26 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.165 Fit side-chains REVERT: H 46 GLU cc_start: 0.8884 (tt0) cc_final: 0.8296 (tt0) REVERT: H 57 TYR cc_start: 0.8965 (m-80) cc_final: 0.8513 (m-80) REVERT: H 78 ILE cc_start: 0.7953 (mp) cc_final: 0.7558 (mp) REVERT: A 155 LYS cc_start: 0.8490 (tttp) cc_final: 0.7400 (mmtt) REVERT: A 191 PHE cc_start: 0.7667 (m-80) cc_final: 0.7208 (m-80) REVERT: A 225 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 304 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6008 (tp) REVERT: A 427 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6575 (ptm-80) REVERT: L 46 LYS cc_start: 0.8801 (ptpt) cc_final: 0.8601 (ptpp) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.0675 time to fit residues: 10.7478 Evaluate side-chains 114 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124761 restraints weight = 7015.355| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.24 r_work: 0.3291 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6044 Z= 0.181 Angle : 0.584 8.114 8219 Z= 0.308 Chirality : 0.042 0.172 899 Planarity : 0.005 0.058 1013 Dihedral : 4.485 17.656 819 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 15.51 % Favored : 81.33 % 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: 0.06 (0.32), residues: 738 helix: 1.14 (0.27), residues: 358 sheet: -1.20 (0.50), residues: 112 loop : -0.81 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.022 0.001 TYR A 137 PHE 0.017 0.002 PHE A 473 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 6041) covalent geometry : angle 0.58352 / 0.31 ( 8213) SS BOND : bond 0.00203 / 0.10 ( 3) SS BOND : angle 0.62300 / 0.31 ( 6) hydrogen bonds : bond 0.04359 / 2.99 ( 316) hydrogen bonds : angle 4.96092 / 3.31 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.191 Fit side-chains REVERT: H 46 GLU cc_start: 0.8889 (tt0) cc_final: 0.8342 (tt0) REVERT: H 57 TYR cc_start: 0.8973 (m-80) cc_final: 0.8455 (m-80) REVERT: H 78 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 155 LYS cc_start: 0.8494 (tttp) cc_final: 0.7402 (mmtt) REVERT: A 191 PHE cc_start: 0.7756 (m-80) cc_final: 0.7353 (m-80) REVERT: A 225 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 304 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6466 (tp) REVERT: A 427 ARG cc_start: 0.6864 (ptm160) cc_final: 0.6551 (ptm-80) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.0743 time to fit residues: 11.3273 Evaluate side-chains 124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125267 restraints weight = 6971.047| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.21 r_work: 0.3286 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6044 Z= 0.173 Angle : 0.572 7.885 8219 Z= 0.302 Chirality : 0.042 0.172 899 Planarity : 0.005 0.057 1013 Dihedral : 4.456 17.820 819 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.64 % Allowed : 16.14 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.32), residues: 738 helix: 1.14 (0.27), residues: 358 sheet: -1.16 (0.50), residues: 112 loop : -0.77 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 240 TYR 0.022 0.001 TYR A 137 PHE 0.014 0.002 PHE A 473 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 6041) covalent geometry : angle 0.57175 / 0.30 ( 8213) SS BOND : bond 0.00251 / 0.12 ( 3) SS BOND : angle 0.64820 / 0.32 ( 6) hydrogen bonds : bond 0.04295 / 2.95 ( 316) hydrogen bonds : angle 4.94414 / 3.29 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8899 (tt0) cc_final: 0.8325 (tt0) REVERT: H 57 TYR cc_start: 0.8969 (m-80) cc_final: 0.8554 (m-80) REVERT: H 78 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 155 LYS cc_start: 0.8492 (tttp) cc_final: 0.7393 (mmtt) REVERT: A 191 PHE cc_start: 0.7842 (m-80) cc_final: 0.7613 (m-10) REVERT: A 225 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 304 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6406 (tp) REVERT: A 322 SER cc_start: 0.8326 (m) cc_final: 0.8003 (p) REVERT: A 427 ARG cc_start: 0.6699 (ptm160) cc_final: 0.6394 (ptm-80) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.0801 time to fit residues: 12.6298 Evaluate side-chains 124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 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 = 0.3775 r_free = 0.3775 target = 0.156055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124548 restraints weight = 7064.900| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.23 r_work: 0.3285 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6044 Z= 0.177 Angle : 0.576 8.052 8219 Z= 0.304 Chirality : 0.042 0.171 899 Planarity : 0.005 0.057 1013 Dihedral : 4.468 17.823 819 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.32 % Allowed : 16.30 % Favored : 80.38 % 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: 0.09 (0.31), residues: 738 helix: 1.13 (0.27), residues: 358 sheet: -1.17 (0.50), residues: 112 loop : -0.75 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 240 TYR 0.022 0.001 TYR A 137 PHE 0.014 0.002 PHE A 455 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 6041) covalent geometry : angle 0.57588 / 0.30 ( 8213) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 0.69293 / 0.34 ( 6) hydrogen bonds : bond 0.04336 / 2.97 ( 316) hydrogen bonds : angle 4.96009 / 3.30 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8917 (tt0) cc_final: 0.8367 (tt0) REVERT: H 57 TYR cc_start: 0.8974 (m-80) cc_final: 0.8562 (m-80) REVERT: H 78 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 155 LYS cc_start: 0.8507 (tttp) cc_final: 0.7413 (mmtt) REVERT: A 191 PHE cc_start: 0.7867 (m-80) cc_final: 0.7448 (m-80) REVERT: A 225 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 304 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6456 (tp) REVERT: A 322 SER cc_start: 0.8318 (m) cc_final: 0.8003 (p) REVERT: A 427 ARG cc_start: 0.6719 (ptm160) cc_final: 0.6420 (ptm-80) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.0769 time to fit residues: 12.2237 Evaluate side-chains 125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 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 = 0.3771 r_free = 0.3771 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125066 restraints weight = 7017.733| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.13 r_work: 0.3286 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6044 Z= 0.177 Angle : 0.574 7.954 8219 Z= 0.304 Chirality : 0.042 0.171 899 Planarity : 0.005 0.056 1013 Dihedral : 4.477 17.903 819 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.16 % Allowed : 16.14 % Favored : 80.70 % 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: 0.07 (0.31), residues: 738 helix: 1.14 (0.27), residues: 358 sheet: -1.22 (0.49), residues: 112 loop : -0.76 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 44 TYR 0.022 0.001 TYR A 137 PHE 0.014 0.002 PHE A 455 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6041) covalent geometry : angle 0.57433 / 0.30 ( 8213) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.66480 / 0.33 ( 6) hydrogen bonds : bond 0.04328 / 2.97 ( 316) hydrogen bonds : angle 4.95506 / 3.30 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8899 (tt0) cc_final: 0.8298 (tt0) REVERT: H 57 TYR cc_start: 0.8970 (m-80) cc_final: 0.8552 (m-80) REVERT: H 78 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 155 LYS cc_start: 0.8496 (tttp) cc_final: 0.7397 (mmtt) REVERT: A 191 PHE cc_start: 0.7850 (m-80) cc_final: 0.7446 (m-80) REVERT: A 225 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 304 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6398 (tp) REVERT: A 322 SER cc_start: 0.8300 (m) cc_final: 0.7977 (p) REVERT: A 427 ARG cc_start: 0.6646 (ptm160) cc_final: 0.6346 (ptm-80) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.0818 time to fit residues: 12.2761 Evaluate side-chains 123 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.157729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127344 restraints weight = 6967.940| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.11 r_work: 0.3315 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6044 Z= 0.148 Angle : 0.554 7.637 8219 Z= 0.292 Chirality : 0.041 0.173 899 Planarity : 0.005 0.055 1013 Dihedral : 4.384 17.507 819 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 16.46 % Favored : 80.38 % 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: 0.16 (0.32), residues: 738 helix: 1.21 (0.27), residues: 359 sheet: -1.14 (0.49), residues: 112 loop : -0.75 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.023 0.001 TYR A 137 PHE 0.013 0.001 PHE A 473 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6041) covalent geometry : angle 0.55354 / 0.29 ( 8213) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.64357 / 0.32 ( 6) hydrogen bonds : bond 0.04119 / 2.84 ( 316) hydrogen bonds : angle 4.87602 / 3.25 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.39 seconds wall clock time: 28 minutes 7.78 seconds (1687.78 seconds total)