Starting phenix.real_space_refine on Thu Jul 24 11:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2025/9kmi_62434.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 42 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3949 2.51 5 N 957 2.21 5 O 1075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4289 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 25, 'TRANS': 512} 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, 11 Unusual residues: {' CL': 1, ' NA': 2, 'TAU': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 4.65, per 1000 atoms: 0.77 Number of scatterers: 6026 At special positions: 0 Unit cell: (74.62, 81.18, 109.06, 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 42 16.00 Na 2 11.00 O 1075 8.00 N 957 7.00 C 3949 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=2.38 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 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: 1.40 Conformation dependent library (CDL) restraints added in 828.2 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 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: 33 helices and 7 sheets defined 55.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 removed outlier: 4.174A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.572A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.806A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.620A pdb=" N LYS A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.523A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.660A pdb=" N ARG A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 247 through 266 Proline residue: A 253 - end of helix removed outlier: 3.547A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.814A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.326A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.630A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.211A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.629A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.676A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) 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: 3.909A 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 removed outlier: 3.895A pdb=" N MET A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.526A pdb=" N TYR A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.585A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.603A pdb=" N LYS A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.573A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.568A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.892A 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 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.562A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.826A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.677A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.354A 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 45 through 49 removed outlier: 5.570A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.69 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: 1739 1.34 - 1.46: 1347 1.46 - 1.57: 3048 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 6195 Sorted by residual: bond pdb=" CB VAL A 227 " pdb=" CG1 VAL A 227 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB TRP A 228 " pdb=" CG TRP A 228 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.47e+00 bond pdb=" CB VAL A 378 " pdb=" CG1 VAL A 378 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB ILE A 139 " pdb=" CG2 ILE A 139 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CG1 ILE A 479 " pdb=" CD1 ILE A 479 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 ... (remaining 6190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8060 2.13 - 4.27: 296 4.27 - 6.40: 43 6.40 - 8.53: 11 8.53 - 10.67: 10 Bond angle restraints: 8420 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 121.54 131.81 -10.27 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C ALA A 303 " pdb=" N ILE A 304 " pdb=" CA ILE A 304 " ideal model delta sigma weight residual 122.88 115.74 7.14 1.76e+00 3.23e-01 1.65e+01 angle pdb=" C GLU A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 122.73 118.98 3.75 9.30e-01 1.16e+00 1.62e+01 angle pdb=" CB ILE A 304 " pdb=" CG1 ILE A 304 " pdb=" CD1 ILE A 304 " ideal model delta sigma weight residual 113.80 106.04 7.76 2.10e+00 2.27e-01 1.37e+01 angle pdb=" C ALA A 189 " pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3191 17.85 - 35.71: 294 35.71 - 53.56: 54 53.56 - 71.41: 10 71.41 - 89.26: 5 Dihedral angle restraints: 3554 sinusoidal: 1362 harmonic: 2192 Sorted by residual: dihedral pdb=" CA ALA A 303 " pdb=" C ALA A 303 " pdb=" N ILE A 304 " pdb=" CA ILE A 304 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N GLU A 429 " pdb=" CA GLU A 429 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+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 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 3551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 851 0.104 - 0.209: 64 0.209 - 0.313: 4 0.313 - 0.418: 0 0.418 - 0.522: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CB VAL A 447 " pdb=" CA VAL A 447 " pdb=" CG1 VAL A 447 " pdb=" CG2 VAL A 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CB THR A 249 " pdb=" CA THR A 249 " pdb=" OG1 THR A 249 " pdb=" CG2 THR A 249 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+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 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 917 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 92 " 0.025 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE L 92 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE L 92 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE L 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE L 92 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL A 129 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL A 129 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 130 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 168 " -0.047 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 169 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.039 5.00e-02 4.00e+02 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1504 2.79 - 3.31: 5588 3.31 - 3.84: 10857 3.84 - 4.37: 13203 4.37 - 4.90: 22377 Nonbonded interactions: 53529 Sorted by model distance: nonbonded pdb=" O ILE A 101 " pdb=" OG1 THR A 105 " model vdw 2.256 3.040 nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.272 3.040 nonbonded pdb=" O TYR A 148 " pdb=" OG SER A 152 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP A 494 " pdb=" OH TYR H 59 " model vdw 2.293 3.040 nonbonded pdb=" O VAL A 485 " pdb=" OG SER A 489 " model vdw 2.312 3.040 ... (remaining 53524 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: 3.430 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.300 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.009 0.348 6198 Z= 0.387 Angle : 1.007 13.772 8426 Z= 0.540 Chirality : 0.059 0.522 920 Planarity : 0.008 0.073 1037 Dihedral : 14.304 89.263 2159 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.27), residues: 756 helix: -1.29 (0.23), residues: 375 sheet: -1.48 (0.48), residues: 111 loop : -1.63 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 218 HIS 0.003 0.001 HIS H 80 PHE 0.062 0.003 PHE L 92 TYR 0.029 0.002 TYR A 137 ARG 0.018 0.001 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.14365 ( 326) hydrogen bonds : angle 7.95679 ( 930) SS BOND : bond 0.20106 ( 3) SS BOND : angle 6.08944 ( 6) covalent geometry : bond 0.00766 ( 6195) covalent geometry : angle 0.99446 ( 8420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.700 Fit side-chains REVERT: A 96 PHE cc_start: 0.7973 (t80) cc_final: 0.7772 (t80) REVERT: A 191 PHE cc_start: 0.8247 (m-80) cc_final: 0.7911 (m-80) REVERT: A 256 MET cc_start: 0.8790 (tpt) cc_final: 0.8447 (tpt) REVERT: A 408 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6704 (mt-10) REVERT: L 90 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1804 time to fit residues: 21.8379 Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124079 restraints weight = 6654.111| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.06 r_work: 0.3305 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6198 Z= 0.172 Angle : 0.610 8.856 8426 Z= 0.322 Chirality : 0.043 0.159 920 Planarity : 0.006 0.055 1037 Dihedral : 5.949 55.448 840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.93 % Allowed : 5.09 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.30), residues: 756 helix: -0.16 (0.25), residues: 379 sheet: -1.45 (0.47), residues: 115 loop : -1.19 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 PHE 0.015 0.002 PHE L 92 TYR 0.021 0.001 TYR A 137 ARG 0.004 0.000 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 326) hydrogen bonds : angle 5.52823 ( 930) SS BOND : bond 0.00283 ( 3) SS BOND : angle 1.18268 ( 6) covalent geometry : bond 0.00402 ( 6195) covalent geometry : angle 0.60901 ( 8420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.690 Fit side-chains REVERT: A 191 PHE cc_start: 0.8235 (m-80) cc_final: 0.7913 (m-80) REVERT: A 256 MET cc_start: 0.8808 (tpt) cc_final: 0.8314 (tpt) REVERT: A 408 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7293 (mt-10) REVERT: H 40 SER cc_start: 0.8128 (t) cc_final: 0.7890 (p) REVERT: L 90 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8269 (tt0) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.1900 time to fit residues: 24.9543 Evaluate side-chains 89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121221 restraints weight = 6761.447| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.02 r_work: 0.3215 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6198 Z= 0.166 Angle : 0.588 9.898 8426 Z= 0.307 Chirality : 0.042 0.161 920 Planarity : 0.005 0.047 1037 Dihedral : 5.762 55.206 840 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.54 % Allowed : 7.72 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.31), residues: 756 helix: 0.29 (0.26), residues: 375 sheet: -1.29 (0.47), residues: 115 loop : -1.07 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.016 0.002 PHE L 92 TYR 0.018 0.001 TYR A 137 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 326) hydrogen bonds : angle 5.21194 ( 930) SS BOND : bond 0.00225 ( 3) SS BOND : angle 1.70453 ( 6) covalent geometry : bond 0.00390 ( 6195) covalent geometry : angle 0.58691 ( 8420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 172 MET cc_start: 0.7608 (ttp) cc_final: 0.7324 (ttm) REVERT: A 191 PHE cc_start: 0.8218 (m-80) cc_final: 0.7936 (m-80) REVERT: A 256 MET cc_start: 0.8801 (tpt) cc_final: 0.8281 (tpt) REVERT: A 304 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6765 (tp) REVERT: A 408 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7284 (mt-10) REVERT: A 486 ASN cc_start: 0.8084 (m-40) cc_final: 0.7777 (m110) REVERT: H 40 SER cc_start: 0.8110 (t) cc_final: 0.7879 (p) REVERT: L 90 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8292 (tt0) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.1830 time to fit residues: 23.0315 Evaluate side-chains 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119104 restraints weight = 6841.135| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.10 r_work: 0.3225 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6198 Z= 0.193 Angle : 0.601 9.714 8426 Z= 0.313 Chirality : 0.043 0.169 920 Planarity : 0.005 0.047 1037 Dihedral : 5.739 57.439 840 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.31 % Allowed : 9.41 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.31), residues: 756 helix: 0.41 (0.26), residues: 375 sheet: -1.13 (0.48), residues: 115 loop : -1.03 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.018 0.002 PHE L 92 TYR 0.019 0.001 TYR A 137 ARG 0.007 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 326) hydrogen bonds : angle 5.12936 ( 930) SS BOND : bond 0.00215 ( 3) SS BOND : angle 1.32354 ( 6) covalent geometry : bond 0.00457 ( 6195) covalent geometry : angle 0.59979 ( 8420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7697 (ttp) cc_final: 0.7336 (ttm) REVERT: A 175 THR cc_start: 0.8844 (p) cc_final: 0.8614 (t) REVERT: A 191 PHE cc_start: 0.8350 (m-80) cc_final: 0.7930 (m-80) REVERT: A 192 THR cc_start: 0.8861 (t) cc_final: 0.8660 (t) REVERT: A 256 MET cc_start: 0.8813 (tpt) cc_final: 0.8328 (tpt) REVERT: A 304 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7109 (tp) REVERT: A 408 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7323 (mt-10) REVERT: H 40 SER cc_start: 0.8158 (t) cc_final: 0.7928 (p) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.2570 time to fit residues: 34.5299 Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122446 restraints weight = 6708.244| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.05 r_work: 0.3106 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 0.037 6198 Z= 0.180 Angle : 0.589 9.784 8426 Z= 0.307 Chirality : 0.043 0.165 920 Planarity : 0.005 0.046 1037 Dihedral : 5.693 59.451 840 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.78 % Allowed : 10.19 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 756 helix: 0.49 (0.26), residues: 377 sheet: -1.04 (0.48), residues: 115 loop : -1.00 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.015 0.002 PHE L 92 TYR 0.018 0.001 TYR A 137 ARG 0.003 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 326) hydrogen bonds : angle 5.04624 ( 930) SS BOND : bond 0.00198 ( 3) SS BOND : angle 1.17602 ( 6) covalent geometry : bond 0.00427 ( 6195) covalent geometry : angle 0.58869 ( 8420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7697 (ttp) cc_final: 0.7266 (ttm) REVERT: A 175 THR cc_start: 0.8810 (p) cc_final: 0.8582 (t) REVERT: A 191 PHE cc_start: 0.8389 (m-80) cc_final: 0.7949 (m-80) REVERT: A 192 THR cc_start: 0.8806 (t) cc_final: 0.8586 (t) REVERT: A 256 MET cc_start: 0.8793 (tpt) cc_final: 0.8295 (tpt) REVERT: A 304 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7243 (tp) REVERT: A 408 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 486 ASN cc_start: 0.8021 (m-40) cc_final: 0.7750 (m-40) REVERT: H 40 SER cc_start: 0.8062 (t) cc_final: 0.7835 (p) REVERT: H 78 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7693 (tt) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.2424 time to fit residues: 34.2560 Evaluate side-chains 103 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 249 THR 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 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121929 restraints weight = 6652.138| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.06 r_work: 0.3078 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6198 Z= 0.196 Angle : 0.613 10.392 8426 Z= 0.316 Chirality : 0.043 0.166 920 Planarity : 0.005 0.046 1037 Dihedral : 5.691 56.749 840 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 10.96 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.31), residues: 756 helix: 0.49 (0.26), residues: 378 sheet: -1.03 (0.48), residues: 115 loop : -0.98 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.016 0.002 PHE L 92 TYR 0.017 0.001 TYR A 137 ARG 0.005 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 326) hydrogen bonds : angle 5.07271 ( 930) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.14979 ( 6) covalent geometry : bond 0.00468 ( 6195) covalent geometry : angle 0.61199 ( 8420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8477 (p90) REVERT: A 172 MET cc_start: 0.7737 (ttp) cc_final: 0.7331 (ttm) REVERT: A 175 THR cc_start: 0.8812 (p) cc_final: 0.8600 (t) REVERT: A 191 PHE cc_start: 0.8442 (m-80) cc_final: 0.8000 (m-80) REVERT: A 256 MET cc_start: 0.8811 (tpt) cc_final: 0.8300 (tpt) REVERT: A 304 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7310 (tp) REVERT: A 486 ASN cc_start: 0.8042 (m-40) cc_final: 0.7761 (m-40) REVERT: H 40 SER cc_start: 0.8045 (t) cc_final: 0.7808 (p) REVERT: H 78 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7702 (tt) REVERT: L 90 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8584 (tm-30) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 0.2438 time to fit residues: 33.8566 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 249 THR 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 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 0.0270 chunk 57 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127484 restraints weight = 6756.778| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.08 r_work: 0.3291 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6198 Z= 0.124 Angle : 0.565 10.448 8426 Z= 0.289 Chirality : 0.040 0.136 920 Planarity : 0.005 0.045 1037 Dihedral : 5.328 50.395 840 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 12.35 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 756 helix: 0.75 (0.27), residues: 379 sheet: -0.98 (0.49), residues: 113 loop : -0.91 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.011 0.001 PHE A 392 TYR 0.017 0.001 TYR A 137 ARG 0.009 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 326) hydrogen bonds : angle 4.78955 ( 930) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.75374 ( 6) covalent geometry : bond 0.00287 ( 6195) covalent geometry : angle 0.56515 ( 8420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8020 (p90) REVERT: A 172 MET cc_start: 0.7554 (ttp) cc_final: 0.7183 (ttm) REVERT: A 191 PHE cc_start: 0.8428 (m-80) cc_final: 0.7935 (m-80) REVERT: A 256 MET cc_start: 0.8808 (tpt) cc_final: 0.8363 (tpt) REVERT: H 78 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7765 (tt) REVERT: L 90 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8478 (tt0) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.2593 time to fit residues: 36.6397 Evaluate side-chains 102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126701 restraints weight = 6648.757| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.09 r_work: 0.3243 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6198 Z= 0.167 Angle : 0.592 10.454 8426 Z= 0.304 Chirality : 0.042 0.144 920 Planarity : 0.005 0.046 1037 Dihedral : 5.346 50.635 840 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.78 % Allowed : 13.43 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 756 helix: 0.72 (0.26), residues: 380 sheet: -0.80 (0.49), residues: 115 loop : -0.94 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.014 0.002 PHE A 392 TYR 0.018 0.001 TYR A 137 ARG 0.007 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 326) hydrogen bonds : angle 4.88879 ( 930) SS BOND : bond 0.00150 ( 3) SS BOND : angle 1.05471 ( 6) covalent geometry : bond 0.00394 ( 6195) covalent geometry : angle 0.59134 ( 8420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.592 Fit side-chains REVERT: A 69 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8174 (p90) REVERT: A 172 MET cc_start: 0.7737 (ttp) cc_final: 0.7319 (ttm) REVERT: A 191 PHE cc_start: 0.8454 (m-80) cc_final: 0.8026 (m-80) REVERT: A 256 MET cc_start: 0.8828 (tpt) cc_final: 0.8350 (tpt) REVERT: A 304 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7146 (tp) REVERT: H 78 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7778 (tt) REVERT: L 90 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8559 (tt0) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.2301 time to fit residues: 32.0016 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124871 restraints weight = 6756.817| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.08 r_work: 0.3129 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6198 Z= 0.159 Angle : 0.589 10.785 8426 Z= 0.302 Chirality : 0.041 0.142 920 Planarity : 0.005 0.045 1037 Dihedral : 5.280 48.957 840 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.93 % Allowed : 13.89 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.32), residues: 756 helix: 0.72 (0.26), residues: 380 sheet: -0.75 (0.50), residues: 115 loop : -0.93 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.014 0.001 PHE A 392 TYR 0.018 0.001 TYR A 137 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 326) hydrogen bonds : angle 4.87168 ( 930) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.97302 ( 6) covalent geometry : bond 0.00376 ( 6195) covalent geometry : angle 0.58824 ( 8420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.664 Fit side-chains REVERT: A 69 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8058 (p90) REVERT: A 256 MET cc_start: 0.8791 (tpt) cc_final: 0.8346 (tpt) REVERT: L 90 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8553 (tt0) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.1853 time to fit residues: 25.3400 Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130053 restraints weight = 6736.508| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.13 r_work: 0.3344 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6198 Z= 0.130 Angle : 0.582 12.320 8426 Z= 0.294 Chirality : 0.040 0.138 920 Planarity : 0.005 0.045 1037 Dihedral : 5.153 47.019 840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.47 % Allowed : 14.04 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 756 helix: 0.82 (0.27), residues: 379 sheet: -0.79 (0.51), residues: 113 loop : -0.89 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 PHE 0.013 0.001 PHE A 191 TYR 0.018 0.001 TYR A 137 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 326) hydrogen bonds : angle 4.77425 ( 930) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.74550 ( 6) covalent geometry : bond 0.00301 ( 6195) covalent geometry : angle 0.58167 ( 8420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.639 Fit side-chains REVERT: A 69 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7782 (p90) REVERT: A 256 MET cc_start: 0.8802 (tpt) cc_final: 0.8396 (tpt) REVERT: A 427 ARG cc_start: 0.6467 (mmm160) cc_final: 0.5695 (mmm160) REVERT: H 93 MET cc_start: 0.7986 (tpp) cc_final: 0.7782 (tpp) REVERT: L 11 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4751 (ptp) REVERT: L 90 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8525 (tt0) outliers start: 16 outliers final: 13 residues processed: 103 average time/residue: 0.1772 time to fit residues: 24.5604 Evaluate side-chains 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127329 restraints weight = 6800.128| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.10 r_work: 0.3288 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6198 Z= 0.138 Angle : 0.587 11.881 8426 Z= 0.297 Chirality : 0.041 0.139 920 Planarity : 0.005 0.045 1037 Dihedral : 5.191 47.941 840 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.31 % Allowed : 14.20 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.32), residues: 756 helix: 0.85 (0.27), residues: 378 sheet: -0.74 (0.50), residues: 118 loop : -0.83 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.001 0.001 HIS H 80 PHE 0.012 0.001 PHE A 392 TYR 0.019 0.001 TYR A 137 ARG 0.009 0.001 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 326) hydrogen bonds : angle 4.76798 ( 930) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.88692 ( 6) covalent geometry : bond 0.00324 ( 6195) covalent geometry : angle 0.58704 ( 8420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.78 seconds wall clock time: 71 minutes 38.49 seconds (4298.49 seconds total)