Starting phenix.real_space_refine on Wed Sep 17 06:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmi_62434/09_2025/9kmi_62434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmi_62434/09_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_62434/09_2025/9kmi_62434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmi_62434/09_2025/9kmi_62434.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmi_62434/09_2025/9kmi_62434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmi_62434/09_2025/9kmi_62434.cif" } resolution = 3.05 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.27 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: 0.52 Conformation dependent library (CDL) restraints added in 331.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.01 Time building geometry restraints manager: 0.69 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: 3.730 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.840 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG H 56 TYR 0.029 0.002 TYR A 137 PHE 0.062 0.003 PHE L 92 TRP 0.016 0.002 TRP A 218 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00766 ( 6195) covalent geometry : angle 0.99446 ( 8420) SS BOND : bond 0.20106 ( 3) SS BOND : angle 6.08944 ( 6) hydrogen bonds : bond 0.14365 ( 326) hydrogen bonds : angle 7.95679 ( 930) *********************** 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 : 0.221 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: 0.0866 time to fit residues: 10.5320 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 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 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124264 restraints weight = 6770.070| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.08 r_work: 0.3306 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1167 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= 0.167 Angle : 0.604 8.819 8426 Z= 0.320 Chirality : 0.042 0.156 920 Planarity : 0.006 0.054 1037 Dihedral : 5.928 55.048 840 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.93 % Allowed : 5.25 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.30), residues: 756 helix: -0.14 (0.25), residues: 379 sheet: -1.44 (0.47), residues: 115 loop : -1.18 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.002 PHE L 92 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6195) covalent geometry : angle 0.60389 ( 8420) SS BOND : bond 0.00260 ( 3) SS BOND : angle 1.16597 ( 6) hydrogen bonds : bond 0.04008 ( 326) hydrogen bonds : angle 5.50648 ( 930) *********************** 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 103 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.229 Fit side-chains REVERT: A 191 PHE cc_start: 0.8246 (m-80) cc_final: 0.7965 (m-80) REVERT: A 256 MET cc_start: 0.8810 (tpt) cc_final: 0.8314 (tpt) REVERT: A 408 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7293 (mt-10) REVERT: H 40 SER cc_start: 0.8132 (t) cc_final: 0.7899 (p) REVERT: L 90 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8253 (tt0) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.0930 time to fit residues: 12.1871 Evaluate side-chains 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.0170 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.157026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126639 restraints weight = 6688.965| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.06 r_work: 0.3331 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6198 Z= 0.140 Angle : 0.572 9.993 8426 Z= 0.298 Chirality : 0.041 0.144 920 Planarity : 0.005 0.049 1037 Dihedral : 5.673 54.519 840 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.39 % Allowed : 7.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.31), residues: 756 helix: 0.40 (0.26), residues: 375 sheet: -1.36 (0.47), residues: 118 loop : -1.02 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.018 0.001 TYR A 137 PHE 0.014 0.001 PHE L 92 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6195) covalent geometry : angle 0.57116 ( 8420) SS BOND : bond 0.00543 ( 3) SS BOND : angle 1.48186 ( 6) hydrogen bonds : bond 0.03656 ( 326) hydrogen bonds : angle 5.11713 ( 930) *********************** 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 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7493 (ttp) cc_final: 0.7249 (ttm) REVERT: A 191 PHE cc_start: 0.8191 (m-80) cc_final: 0.7932 (m-80) REVERT: A 201 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8232 (mtp85) REVERT: A 256 MET cc_start: 0.8800 (tpt) cc_final: 0.8347 (tpt) REVERT: A 304 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6835 (tp) REVERT: A 486 ASN cc_start: 0.8019 (m-40) cc_final: 0.7678 (m110) REVERT: H 40 SER cc_start: 0.8124 (t) cc_final: 0.7902 (p) REVERT: L 90 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8236 (tt0) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.0920 time to fit residues: 12.2257 Evaluate side-chains 94 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.0000 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.3502 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.152725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121766 restraints weight = 6773.406| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.06 r_work: 0.3193 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6198 Z= 0.132 Angle : 0.553 9.141 8426 Z= 0.289 Chirality : 0.041 0.138 920 Planarity : 0.005 0.051 1037 Dihedral : 5.489 55.252 840 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.16 % Allowed : 10.19 % Favored : 87.65 % 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 aren not related in a simple way. whole: -0.36 (0.31), residues: 756 helix: 0.65 (0.27), residues: 377 sheet: -1.09 (0.47), residues: 118 loop : -0.97 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 428 TYR 0.018 0.001 TYR A 137 PHE 0.012 0.001 PHE L 92 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6195) covalent geometry : angle 0.55235 ( 8420) SS BOND : bond 0.00178 ( 3) SS BOND : angle 1.28427 ( 6) hydrogen bonds : bond 0.03550 ( 326) hydrogen bonds : angle 4.90711 ( 930) *********************** 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 104 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7320 (ttp) cc_final: 0.6932 (ttm) REVERT: A 191 PHE cc_start: 0.8245 (m-80) cc_final: 0.7878 (m-80) REVERT: A 256 MET cc_start: 0.8798 (tpt) cc_final: 0.8343 (tpt) REVERT: A 304 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.7006 (tp) REVERT: A 327 MET cc_start: 0.8681 (mmm) cc_final: 0.8352 (mmp) REVERT: H 60 TYR cc_start: 0.8824 (m-80) cc_final: 0.8620 (m-80) REVERT: L 90 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8264 (tt0) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 0.0763 time to fit residues: 10.1647 Evaluate side-chains 96 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 249 THR 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 485 VAL Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124176 restraints weight = 6852.692| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.11 r_work: 0.3276 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6198 Z= 0.174 Angle : 0.587 9.638 8426 Z= 0.305 Chirality : 0.042 0.170 920 Planarity : 0.005 0.047 1037 Dihedral : 5.526 56.384 840 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.62 % Allowed : 11.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.31), residues: 756 helix: 0.61 (0.27), residues: 378 sheet: -0.83 (0.50), residues: 109 loop : -1.01 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.019 0.001 TYR A 137 PHE 0.017 0.002 PHE L 92 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6195) covalent geometry : angle 0.58653 ( 8420) SS BOND : bond 0.00181 ( 3) SS BOND : angle 1.26183 ( 6) hydrogen bonds : bond 0.03737 ( 326) hydrogen bonds : angle 4.96747 ( 930) *********************** 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 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7351 (ttp) cc_final: 0.7036 (ttm) REVERT: A 191 PHE cc_start: 0.8357 (m-80) cc_final: 0.7994 (m-80) REVERT: A 212 ASN cc_start: 0.8226 (t0) cc_final: 0.7971 (t0) REVERT: A 256 MET cc_start: 0.8833 (tpt) cc_final: 0.8338 (tpt) REVERT: A 304 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7224 (tp) REVERT: A 327 MET cc_start: 0.8825 (mmm) cc_final: 0.8489 (mmp) REVERT: A 486 ASN cc_start: 0.8087 (m-40) cc_final: 0.7771 (m110) REVERT: H 40 SER cc_start: 0.8098 (t) cc_final: 0.7884 (p) REVERT: H 78 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7780 (tt) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.0931 time to fit residues: 12.5349 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 H residue 78 ILE 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 54 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121635 restraints weight = 6817.225| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.13 r_work: 0.3310 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6198 Z= 0.158 Angle : 0.576 10.507 8426 Z= 0.298 Chirality : 0.042 0.164 920 Planarity : 0.005 0.044 1037 Dihedral : 5.480 58.770 840 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.31), residues: 756 helix: 0.66 (0.27), residues: 379 sheet: -0.87 (0.49), residues: 115 loop : -0.97 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.018 0.001 TYR A 137 PHE 0.014 0.001 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6195) covalent geometry : angle 0.57543 ( 8420) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.07704 ( 6) hydrogen bonds : bond 0.03644 ( 326) hydrogen bonds : angle 4.91750 ( 930) *********************** 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 : 0.233 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7413 (ttp) cc_final: 0.7021 (ttm) REVERT: A 191 PHE cc_start: 0.8339 (m-80) cc_final: 0.7840 (m-80) REVERT: A 212 ASN cc_start: 0.8085 (t0) cc_final: 0.7837 (t0) REVERT: A 256 MET cc_start: 0.8777 (tpt) cc_final: 0.8288 (tpt) REVERT: A 327 MET cc_start: 0.8783 (mmm) cc_final: 0.8414 (mmp) REVERT: A 486 ASN cc_start: 0.7947 (m-40) cc_final: 0.7589 (m110) REVERT: H 40 SER cc_start: 0.8021 (t) cc_final: 0.7799 (p) REVERT: H 60 TYR cc_start: 0.8845 (m-80) cc_final: 0.8643 (m-80) REVERT: H 78 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7677 (tt) REVERT: L 90 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8549 (tm-30) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.0827 time to fit residues: 11.2272 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 H residue 78 ILE 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 28 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121627 restraints weight = 6771.925| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.09 r_work: 0.3171 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6198 Z= 0.209 Angle : 0.616 10.754 8426 Z= 0.319 Chirality : 0.043 0.165 920 Planarity : 0.005 0.048 1037 Dihedral : 5.615 59.800 840 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.24 % Allowed : 11.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 756 helix: 0.53 (0.26), residues: 378 sheet: -0.87 (0.49), residues: 115 loop : -0.94 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.018 0.002 TYR A 137 PHE 0.018 0.002 PHE L 92 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 6195) covalent geometry : angle 0.61519 ( 8420) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.38099 ( 6) hydrogen bonds : bond 0.03886 ( 326) hydrogen bonds : angle 5.06589 ( 930) *********************** 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 114 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7716 (ttp) cc_final: 0.7278 (ttm) REVERT: A 191 PHE cc_start: 0.8432 (m-80) cc_final: 0.7969 (m-80) REVERT: A 256 MET cc_start: 0.8823 (tpt) cc_final: 0.8342 (tpt) REVERT: A 304 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 486 ASN cc_start: 0.8113 (m-40) cc_final: 0.7843 (m-40) REVERT: H 40 SER cc_start: 0.8112 (t) cc_final: 0.7868 (p) REVERT: H 78 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7757 (tt) REVERT: L 90 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8671 (tm-30) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.0860 time to fit residues: 11.8541 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 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 H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124590 restraints weight = 6773.183| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.10 r_work: 0.3336 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6198 Z= 0.130 Angle : 0.565 10.468 8426 Z= 0.290 Chirality : 0.041 0.150 920 Planarity : 0.005 0.044 1037 Dihedral : 5.311 55.413 840 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.47 % Allowed : 13.12 % Favored : 84.41 % 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 aren not related in a simple way. whole: -0.18 (0.31), residues: 756 helix: 0.75 (0.27), residues: 379 sheet: -0.90 (0.50), residues: 113 loop : -0.89 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 428 TYR 0.017 0.001 TYR A 137 PHE 0.012 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6195) covalent geometry : angle 0.56426 ( 8420) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.97050 ( 6) hydrogen bonds : bond 0.03488 ( 326) hydrogen bonds : angle 4.82078 ( 930) *********************** 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 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.244 Fit side-chains REVERT: A 69 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 256 MET cc_start: 0.8821 (tpt) cc_final: 0.8396 (tpt) REVERT: A 304 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7251 (tp) REVERT: A 327 MET cc_start: 0.8792 (mmm) cc_final: 0.8450 (mmp) REVERT: A 486 ASN cc_start: 0.7936 (m-40) cc_final: 0.7570 (m110) REVERT: A 495 MET cc_start: 0.8961 (ptt) cc_final: 0.8544 (ptt) REVERT: H 40 SER cc_start: 0.8027 (t) cc_final: 0.7827 (p) REVERT: H 60 TYR cc_start: 0.8808 (m-80) cc_final: 0.8607 (m-80) REVERT: L 90 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8574 (tm-30) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.0821 time to fit residues: 11.1676 Evaluate side-chains 104 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS 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 304 ILE Chi-restraints excluded: chain A residue 328 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 65 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128029 restraints weight = 6811.255| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.10 r_work: 0.3353 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6198 Z= 0.124 Angle : 0.559 11.847 8426 Z= 0.286 Chirality : 0.041 0.143 920 Planarity : 0.005 0.044 1037 Dihedral : 5.171 55.422 840 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % 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 aren not related in a simple way. whole: -0.03 (0.32), residues: 756 helix: 0.85 (0.27), residues: 380 sheet: -0.73 (0.50), residues: 118 loop : -0.84 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.019 0.001 TYR A 137 PHE 0.012 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6195) covalent geometry : angle 0.55881 ( 8420) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.94634 ( 6) hydrogen bonds : bond 0.03428 ( 326) hydrogen bonds : angle 4.71401 ( 930) *********************** 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 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.235 Fit side-chains REVERT: A 69 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8019 (p90) REVERT: A 191 PHE cc_start: 0.7752 (m-80) cc_final: 0.7551 (m-80) REVERT: A 256 MET cc_start: 0.8808 (tpt) cc_final: 0.8419 (tpt) REVERT: A 304 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.6860 (tp) REVERT: A 327 MET cc_start: 0.8772 (mmm) cc_final: 0.8477 (mmp) REVERT: A 427 ARG cc_start: 0.6501 (mmm160) cc_final: 0.5731 (mmm160) REVERT: A 486 ASN cc_start: 0.7913 (m-40) cc_final: 0.7529 (m-40) REVERT: L 90 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8452 (tt0) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.0845 time to fit residues: 11.9966 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 236 TRP 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 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 44 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124802 restraints weight = 6787.744| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.09 r_work: 0.3131 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2025 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= 0.162 Angle : 0.584 12.068 8426 Z= 0.302 Chirality : 0.041 0.142 920 Planarity : 0.005 0.044 1037 Dihedral : 5.298 55.656 840 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.47 % Allowed : 13.12 % Favored : 84.41 % 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 aren not related in a simple way. whole: -0.11 (0.32), residues: 756 helix: 0.75 (0.27), residues: 380 sheet: -0.56 (0.51), residues: 115 loop : -0.93 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.020 0.001 TYR A 137 PHE 0.014 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6195) covalent geometry : angle 0.58293 ( 8420) SS BOND : bond 0.00123 ( 3) SS BOND : angle 1.23557 ( 6) hydrogen bonds : bond 0.03630 ( 326) hydrogen bonds : angle 4.81381 ( 930) ********************** 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 109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.231 Fit side-chains REVERT: A 69 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8132 (p90) REVERT: A 256 MET cc_start: 0.8768 (tpt) cc_final: 0.8328 (tpt) REVERT: A 304 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 327 MET cc_start: 0.8799 (mmm) cc_final: 0.8532 (mmp) REVERT: A 427 ARG cc_start: 0.6442 (mmm160) cc_final: 0.5712 (mmt-90) REVERT: A 486 ASN cc_start: 0.7920 (m-40) cc_final: 0.7567 (m-40) REVERT: L 11 MET cc_start: 0.5166 (OUTLIER) cc_final: 0.4779 (ptp) REVERT: L 90 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8469 (tt0) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.0916 time to fit residues: 12.3099 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 236 TRP 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 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 73 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124488 restraints weight = 6753.045| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.10 r_work: 0.3293 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6198 Z= 0.161 Angle : 0.586 11.911 8426 Z= 0.302 Chirality : 0.041 0.142 920 Planarity : 0.005 0.044 1037 Dihedral : 5.325 54.776 840 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.62 % Allowed : 13.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.31), residues: 756 helix: 0.73 (0.27), residues: 380 sheet: -0.54 (0.51), residues: 115 loop : -0.96 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 428 TYR 0.020 0.001 TYR A 137 PHE 0.017 0.002 PHE A 191 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6195) covalent geometry : angle 0.58505 ( 8420) SS BOND : bond 0.00111 ( 3) SS BOND : angle 1.25880 ( 6) hydrogen bonds : bond 0.03628 ( 326) hydrogen bonds : angle 4.82776 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.40 seconds wall clock time: 31 minutes 3.56 seconds (1863.56 seconds total)