Starting phenix.real_space_refine on Fri Dec 27 12:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9f_32366/12_2024/7w9f_32366.cif" } resolution = 3.6 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= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3066 2.51 5 N 807 2.21 5 O 961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4856 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1671 Classifications: {'peptide': 220} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 3.45, per 1000 atoms: 0.71 Number of scatterers: 4856 At special positions: 0 Unit cell: (63.394, 92.905, 137.718, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 961 8.00 N 807 7.00 C 3066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 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: 1.19 Conformation dependent library (CDL) restraints added in 977.6 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 7.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 4.070A pdb=" N LYS A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.627A pdb=" N ASP A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.627A pdb=" N TYR A 104 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.796A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'E' and resid 337 through 343 removed outlier: 4.003A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.759A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 22 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 79 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLU A 10 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 117 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 40 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 45 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 50 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 59 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.657A pdb=" N VAL A 143 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 188 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 147 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 186 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 182 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.657A pdb=" N VAL A 143 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 188 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 147 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 186 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 182 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.663A pdb=" N THR A 211 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.675A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.729A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.841A pdb=" N ASN B 137 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.792A pdb=" N ASN B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 149 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.966A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 397 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'E' and resid 473 through 474 125 hydrogen bonds defined for protein. 303 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: 1.31 Time building geometry restraints manager: 1.40 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: 1538 1.34 - 1.46: 1249 1.46 - 1.58: 2167 1.58 - 1.70: 0 1.70 - 1.81: 28 Bond restraints: 4982 Sorted by residual: bond pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 1.516 1.539 -0.023 1.42e-02 4.96e+03 2.55e+00 bond pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.48e-02 4.57e+03 2.22e+00 bond pdb=" C PRO A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.40e-02 5.10e+03 2.07e+00 bond pdb=" C TYR A 101 " pdb=" N PRO A 102 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.45e+00 bond pdb=" CB LYS E 458 " pdb=" CG LYS E 458 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 4977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 6628 2.14 - 4.27: 135 4.27 - 6.41: 16 6.41 - 8.54: 5 8.54 - 10.68: 1 Bond angle restraints: 6785 Sorted by residual: angle pdb=" C PRO A 133 " pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 121.70 132.38 -10.68 1.80e+00 3.09e-01 3.52e+01 angle pdb=" C SER B 50 " pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 122.61 129.74 -7.13 1.56e+00 4.11e-01 2.09e+01 angle pdb=" CA PRO A 133 " pdb=" C PRO A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 117.98 123.82 -5.84 1.43e+00 4.89e-01 1.67e+01 angle pdb=" N PRO A 133 " pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 113.40 118.54 -5.14 1.34e+00 5.57e-01 1.47e+01 angle pdb=" C GLY A 100 " pdb=" N TYR A 101 " pdb=" CA TYR A 101 " ideal model delta sigma weight residual 120.09 123.38 -3.29 1.25e+00 6.40e-01 6.95e+00 ... (remaining 6780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2672 17.92 - 35.83: 239 35.83 - 53.75: 36 53.75 - 71.66: 8 71.66 - 89.58: 4 Dihedral angle restraints: 2959 sinusoidal: 1136 harmonic: 1823 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 143.74 -50.74 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 140.42 -47.42 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA TYR A 105 " pdb=" C TYR A 105 " pdb=" N ALA A 106 " pdb=" CA ALA A 106 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 585 0.058 - 0.116: 133 0.116 - 0.174: 19 0.174 - 0.232: 3 0.232 - 0.289: 2 Chirality restraints: 742 Sorted by residual: chirality pdb=" CB ILE E 468 " pdb=" CA ILE E 468 " pdb=" CG1 ILE E 468 " pdb=" CG2 ILE E 468 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PRO A 133 " pdb=" N PRO A 133 " pdb=" C PRO A 133 " pdb=" CB PRO A 133 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 739 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 155 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 156 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 101 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 102 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO E 463 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " -0.026 5.00e-02 4.00e+02 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1574 2.82 - 3.34: 3720 3.34 - 3.86: 7775 3.86 - 4.38: 8405 4.38 - 4.90: 14864 Nonbonded interactions: 36338 Sorted by model distance: nonbonded pdb=" OD1 ASP B 82 " pdb=" OH TYR B 86 " model vdw 2.302 3.040 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.322 3.040 nonbonded pdb=" O ILE B 150 " pdb=" OG SER B 153 " model vdw 2.325 3.040 nonbonded pdb=" O SER B 171 " pdb=" OG SER B 171 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.354 3.040 ... (remaining 36333 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 group one per residue 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: 0.360 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.003 0.034 4982 Z= 0.226 Angle : 0.729 10.679 6785 Z= 0.395 Chirality : 0.051 0.289 742 Planarity : 0.006 0.048 874 Dihedral : 13.990 89.579 1775 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -3.66 (0.28), residues: 619 helix: -5.15 (0.17), residues: 28 sheet: -1.84 (0.29), residues: 249 loop : -2.69 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 195 HIS 0.002 0.001 HIS B 189 PHE 0.013 0.001 PHE E 400 TYR 0.010 0.001 TYR B 49 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6403 (ttm) cc_final: 0.5698 (tpp) REVERT: A 81 MET cc_start: 0.8461 (ttp) cc_final: 0.8202 (ttm) REVERT: A 95 TYR cc_start: 0.8091 (m-80) cc_final: 0.7569 (m-80) REVERT: A 129 TYR cc_start: 0.7631 (m-80) cc_final: 0.7320 (m-80) REVERT: A 142 MET cc_start: 0.8006 (mtm) cc_final: 0.7625 (mmt) REVERT: B 11 MET cc_start: 0.7820 (mtm) cc_final: 0.7580 (mtt) REVERT: B 107 LYS cc_start: 0.8695 (mttt) cc_final: 0.8449 (ttmm) REVERT: B 108 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7795 (ttt-90) REVERT: E 360 ASN cc_start: 0.7111 (t0) cc_final: 0.6814 (t0) REVERT: E 414 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8211 (mp10) REVERT: E 505 TYR cc_start: 0.7385 (t80) cc_final: 0.7136 (t80) REVERT: E 508 TYR cc_start: 0.7257 (m-80) cc_final: 0.6949 (m-80) REVERT: E 511 VAL cc_start: 0.8341 (t) cc_final: 0.8047 (m) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1719 time to fit residues: 30.0281 Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 140 ASN B 8 GLN B 124 GLN B 138 ASN B 190 ASN E 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4982 Z= 0.265 Angle : 0.584 6.935 6785 Z= 0.311 Chirality : 0.044 0.177 742 Planarity : 0.005 0.060 874 Dihedral : 4.603 29.607 685 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 12.27 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -2.74 (0.30), residues: 619 helix: -4.77 (0.22), residues: 33 sheet: -1.14 (0.30), residues: 248 loop : -2.04 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 436 HIS 0.002 0.001 HIS E 519 PHE 0.015 0.002 PHE E 347 TYR 0.021 0.002 TYR E 351 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8304 (mtpp) REVERT: A 34 MET cc_start: 0.6364 (ttm) cc_final: 0.5732 (tpp) REVERT: A 115 SER cc_start: 0.7749 (t) cc_final: 0.7246 (p) REVERT: A 129 TYR cc_start: 0.7727 (m-80) cc_final: 0.7480 (m-80) REVERT: A 142 MET cc_start: 0.8016 (mtm) cc_final: 0.7638 (mmt) REVERT: A 186 SER cc_start: 0.8581 (m) cc_final: 0.8321 (p) REVERT: B 9 LYS cc_start: 0.7786 (mttt) cc_final: 0.7492 (mttt) REVERT: B 11 MET cc_start: 0.7779 (mtm) cc_final: 0.7537 (mtt) REVERT: B 108 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7880 (ttt-90) REVERT: B 206 VAL cc_start: 0.7345 (t) cc_final: 0.7035 (p) REVERT: E 341 VAL cc_start: 0.8315 (m) cc_final: 0.8115 (t) REVERT: E 360 ASN cc_start: 0.7742 (t0) cc_final: 0.7389 (t0) REVERT: E 394 ASN cc_start: 0.8450 (p0) cc_final: 0.8133 (p0) REVERT: E 414 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8060 (mp10) REVERT: E 508 TYR cc_start: 0.7232 (m-80) cc_final: 0.6921 (m-80) REVERT: E 512 VAL cc_start: 0.7705 (t) cc_final: 0.7468 (p) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.1393 time to fit residues: 25.2857 Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4982 Z= 0.206 Angle : 0.564 7.349 6785 Z= 0.294 Chirality : 0.044 0.171 742 Planarity : 0.004 0.062 874 Dihedral : 4.387 26.197 685 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.01 % Allowed : 16.85 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -2.22 (0.32), residues: 619 helix: -4.28 (0.39), residues: 33 sheet: -0.83 (0.31), residues: 253 loop : -1.67 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 436 HIS 0.002 0.000 HIS E 519 PHE 0.010 0.001 PHE E 347 TYR 0.025 0.002 TYR B 140 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7817 (t) cc_final: 0.7328 (p) REVERT: A 129 TYR cc_start: 0.7720 (m-80) cc_final: 0.7425 (m-80) REVERT: A 142 MET cc_start: 0.7966 (mtm) cc_final: 0.7554 (mmt) REVERT: A 186 SER cc_start: 0.8546 (m) cc_final: 0.8261 (p) REVERT: B 9 LYS cc_start: 0.7730 (mttt) cc_final: 0.7457 (mttt) REVERT: B 11 MET cc_start: 0.7840 (mtm) cc_final: 0.7631 (mtt) REVERT: B 107 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8273 (ttmm) REVERT: B 108 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7764 (ttt-90) REVERT: E 341 VAL cc_start: 0.8362 (m) cc_final: 0.8136 (t) REVERT: E 360 ASN cc_start: 0.7790 (t0) cc_final: 0.7379 (t0) REVERT: E 365 TYR cc_start: 0.8325 (m-10) cc_final: 0.7962 (m-10) REVERT: E 394 ASN cc_start: 0.8677 (p0) cc_final: 0.8257 (p0) REVERT: E 414 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8044 (mp10) REVERT: E 505 TYR cc_start: 0.7424 (t80) cc_final: 0.6985 (t80) REVERT: E 508 TYR cc_start: 0.7263 (m-80) cc_final: 0.6966 (m-80) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.1580 time to fit residues: 28.7619 Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4982 Z= 0.192 Angle : 0.547 6.653 6785 Z= 0.283 Chirality : 0.043 0.168 742 Planarity : 0.004 0.064 874 Dihedral : 4.336 24.277 685 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 17.77 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.92 (0.32), residues: 619 helix: -3.93 (0.51), residues: 34 sheet: -0.64 (0.31), residues: 253 loop : -1.46 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.002 0.000 HIS E 519 PHE 0.018 0.001 PHE E 374 TYR 0.027 0.002 TYR B 140 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.6982 (tpp) cc_final: 0.6518 (tpp) REVERT: A 115 SER cc_start: 0.7824 (t) cc_final: 0.7326 (p) REVERT: A 129 TYR cc_start: 0.7762 (m-80) cc_final: 0.7481 (m-80) REVERT: A 142 MET cc_start: 0.7933 (mtm) cc_final: 0.7437 (mmp) REVERT: A 186 SER cc_start: 0.8538 (m) cc_final: 0.8253 (p) REVERT: B 9 LYS cc_start: 0.7749 (mttt) cc_final: 0.7469 (mttt) REVERT: B 107 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8205 (mttp) REVERT: B 108 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7963 (ttt-90) REVERT: E 341 VAL cc_start: 0.8388 (m) cc_final: 0.8152 (t) REVERT: E 360 ASN cc_start: 0.7878 (t0) cc_final: 0.7470 (t0) REVERT: E 365 TYR cc_start: 0.8195 (m-10) cc_final: 0.7790 (m-10) REVERT: E 398 ASP cc_start: 0.6646 (m-30) cc_final: 0.6232 (m-30) REVERT: E 406 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6968 (mp0) REVERT: E 414 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8031 (mp10) REVERT: E 505 TYR cc_start: 0.7466 (t80) cc_final: 0.7029 (t80) REVERT: E 508 TYR cc_start: 0.7282 (m-80) cc_final: 0.6982 (m-80) REVERT: E 511 VAL cc_start: 0.8419 (t) cc_final: 0.8146 (m) outliers start: 14 outliers final: 12 residues processed: 140 average time/residue: 0.1714 time to fit residues: 30.7842 Evaluate side-chains 145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4982 Z= 0.476 Angle : 0.682 7.680 6785 Z= 0.355 Chirality : 0.047 0.185 742 Planarity : 0.005 0.065 874 Dihedral : 5.131 34.465 685 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.48 % Allowed : 19.05 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -2.01 (0.32), residues: 619 helix: -3.52 (0.64), residues: 33 sheet: -0.59 (0.31), residues: 250 loop : -1.69 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 436 HIS 0.004 0.001 HIS A 109 PHE 0.014 0.002 PHE E 400 TYR 0.028 0.003 TYR B 140 ARG 0.003 0.001 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8215 (m-80) cc_final: 0.7924 (m-80) REVERT: A 115 SER cc_start: 0.7889 (t) cc_final: 0.7338 (p) REVERT: A 129 TYR cc_start: 0.7871 (m-80) cc_final: 0.7634 (m-80) REVERT: A 142 MET cc_start: 0.7955 (mtm) cc_final: 0.7470 (mmp) REVERT: A 181 LEU cc_start: 0.7582 (mt) cc_final: 0.7352 (tp) REVERT: A 186 SER cc_start: 0.8661 (m) cc_final: 0.8390 (p) REVERT: B 9 LYS cc_start: 0.7810 (mttt) cc_final: 0.7541 (mttt) REVERT: B 107 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8135 (ttmm) REVERT: B 108 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7755 (ttt-90) REVERT: B 175 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7310 (ttt) REVERT: E 341 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (t) REVERT: E 360 ASN cc_start: 0.8222 (t0) cc_final: 0.7783 (t0) REVERT: E 398 ASP cc_start: 0.6702 (m-30) cc_final: 0.6351 (m-30) REVERT: E 414 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7838 (mp10) REVERT: E 508 TYR cc_start: 0.7245 (m-80) cc_final: 0.6931 (m-80) REVERT: E 511 VAL cc_start: 0.8645 (t) cc_final: 0.8236 (m) outliers start: 19 outliers final: 10 residues processed: 143 average time/residue: 0.1610 time to fit residues: 29.6199 Evaluate side-chains 150 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4982 Z= 0.178 Angle : 0.559 6.637 6785 Z= 0.290 Chirality : 0.043 0.164 742 Planarity : 0.004 0.066 874 Dihedral : 4.514 23.964 685 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.93 % Allowed : 19.96 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.75 (0.33), residues: 619 helix: -3.50 (0.63), residues: 35 sheet: -0.46 (0.32), residues: 251 loop : -1.44 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 436 HIS 0.001 0.001 HIS B 189 PHE 0.020 0.001 PHE E 347 TYR 0.028 0.002 TYR B 140 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7704 (m100) cc_final: 0.7311 (m100) REVERT: A 115 SER cc_start: 0.7830 (t) cc_final: 0.7340 (p) REVERT: A 129 TYR cc_start: 0.7834 (m-80) cc_final: 0.7632 (m-80) REVERT: A 142 MET cc_start: 0.7868 (mtm) cc_final: 0.7362 (mmp) REVERT: A 186 SER cc_start: 0.8588 (m) cc_final: 0.8313 (p) REVERT: B 4 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7020 (ttt) REVERT: B 9 LYS cc_start: 0.7739 (mttt) cc_final: 0.7479 (mttt) REVERT: B 107 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8164 (ttmm) REVERT: B 108 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7945 (ttt-90) REVERT: B 123 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8351 (mp0) REVERT: B 175 MET cc_start: 0.7338 (ttp) cc_final: 0.7050 (ttt) REVERT: B 206 VAL cc_start: 0.7283 (t) cc_final: 0.7020 (p) REVERT: E 341 VAL cc_start: 0.8418 (m) cc_final: 0.8194 (t) REVERT: E 360 ASN cc_start: 0.8017 (t0) cc_final: 0.7541 (t0) REVERT: E 414 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7756 (mp10) REVERT: E 423 TYR cc_start: 0.7140 (t80) cc_final: 0.6863 (t80) REVERT: E 433 VAL cc_start: 0.7969 (p) cc_final: 0.7618 (m) REVERT: E 508 TYR cc_start: 0.7234 (m-80) cc_final: 0.7034 (m-80) REVERT: E 511 VAL cc_start: 0.8557 (t) cc_final: 0.8140 (m) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.1477 time to fit residues: 27.4444 Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4982 Z= 0.179 Angle : 0.556 8.289 6785 Z= 0.288 Chirality : 0.043 0.165 742 Planarity : 0.004 0.065 874 Dihedral : 4.512 33.185 685 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.56 % Allowed : 20.33 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.53 (0.33), residues: 619 helix: -3.40 (0.65), residues: 34 sheet: -0.28 (0.32), residues: 251 loop : -1.32 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.001 HIS A 109 PHE 0.012 0.001 PHE E 374 TYR 0.023 0.002 TYR B 140 ARG 0.001 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8202 (m-80) cc_final: 0.7735 (m-80) REVERT: A 110 TRP cc_start: 0.7721 (m100) cc_final: 0.7377 (m100) REVERT: A 115 SER cc_start: 0.7847 (t) cc_final: 0.7349 (p) REVERT: A 129 TYR cc_start: 0.7849 (m-80) cc_final: 0.7632 (m-80) REVERT: A 142 MET cc_start: 0.7848 (mtm) cc_final: 0.7349 (mmp) REVERT: A 186 SER cc_start: 0.8577 (m) cc_final: 0.8275 (p) REVERT: B 4 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7054 (ttt) REVERT: B 9 LYS cc_start: 0.7740 (mttt) cc_final: 0.7495 (mttt) REVERT: B 107 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8153 (ttmm) REVERT: B 108 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7935 (ttt-90) REVERT: B 123 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8340 (mp0) REVERT: B 175 MET cc_start: 0.7346 (ttp) cc_final: 0.7101 (ttt) REVERT: E 341 VAL cc_start: 0.8463 (m) cc_final: 0.8230 (t) REVERT: E 360 ASN cc_start: 0.8052 (t0) cc_final: 0.7568 (t0) REVERT: E 396 TYR cc_start: 0.6990 (m-10) cc_final: 0.6783 (m-10) REVERT: E 398 ASP cc_start: 0.6602 (m-30) cc_final: 0.6381 (m-30) REVERT: E 406 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7164 (mt-10) REVERT: E 414 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7682 (mp10) REVERT: E 433 VAL cc_start: 0.7911 (p) cc_final: 0.7604 (m) REVERT: E 511 VAL cc_start: 0.8538 (t) cc_final: 0.8109 (m) outliers start: 14 outliers final: 11 residues processed: 146 average time/residue: 0.1613 time to fit residues: 30.2612 Evaluate side-chains 147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4982 Z= 0.378 Angle : 0.660 9.897 6785 Z= 0.337 Chirality : 0.045 0.180 742 Planarity : 0.005 0.066 874 Dihedral : 5.083 41.017 685 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.38 % Allowed : 21.43 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.65 (0.33), residues: 619 helix: -3.19 (0.68), residues: 35 sheet: -0.36 (0.33), residues: 251 loop : -1.42 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 436 HIS 0.002 0.001 HIS E 519 PHE 0.012 0.002 PHE E 400 TYR 0.031 0.002 TYR B 140 ARG 0.003 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.481 Fit side-chains REVERT: A 115 SER cc_start: 0.7892 (t) cc_final: 0.7351 (p) REVERT: A 142 MET cc_start: 0.7921 (mtm) cc_final: 0.7428 (mmp) REVERT: A 186 SER cc_start: 0.8632 (m) cc_final: 0.8319 (p) REVERT: B 4 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7113 (ttt) REVERT: B 9 LYS cc_start: 0.7788 (mttt) cc_final: 0.7515 (mttt) REVERT: B 107 LYS cc_start: 0.8352 (ttmm) cc_final: 0.8137 (ttmm) REVERT: B 108 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7936 (ttt-90) REVERT: B 123 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8412 (mp0) REVERT: B 175 MET cc_start: 0.7536 (ttp) cc_final: 0.7335 (ttt) REVERT: E 341 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8332 (t) REVERT: E 360 ASN cc_start: 0.8196 (t0) cc_final: 0.7723 (t0) REVERT: E 406 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 414 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7680 (mp10) REVERT: E 511 VAL cc_start: 0.8616 (t) cc_final: 0.8209 (m) outliers start: 13 outliers final: 10 residues processed: 137 average time/residue: 0.1488 time to fit residues: 26.7263 Evaluate side-chains 141 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.0010 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4982 Z= 0.166 Angle : 0.586 8.404 6785 Z= 0.301 Chirality : 0.044 0.163 742 Planarity : 0.004 0.068 874 Dihedral : 4.579 32.418 685 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.01 % Allowed : 21.79 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.49 (0.34), residues: 619 helix: -3.53 (0.58), residues: 40 sheet: -0.21 (0.33), residues: 250 loop : -1.24 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.002 0.001 HIS A 109 PHE 0.010 0.001 PHE E 347 TYR 0.026 0.002 TYR B 140 ARG 0.002 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.496 Fit side-chains REVERT: A 95 TYR cc_start: 0.8195 (m-80) cc_final: 0.7926 (m-80) REVERT: A 115 SER cc_start: 0.7873 (t) cc_final: 0.7330 (p) REVERT: A 142 MET cc_start: 0.7841 (mtm) cc_final: 0.7376 (mmp) REVERT: A 186 SER cc_start: 0.8535 (m) cc_final: 0.8268 (p) REVERT: B 9 LYS cc_start: 0.7713 (mttt) cc_final: 0.7475 (mttt) REVERT: B 107 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8157 (ttmm) REVERT: B 108 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7936 (ttt-90) REVERT: B 123 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8352 (mp0) REVERT: E 341 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (t) REVERT: E 360 ASN cc_start: 0.8050 (t0) cc_final: 0.7551 (t0) REVERT: E 394 ASN cc_start: 0.8430 (p0) cc_final: 0.8018 (p0) REVERT: E 406 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7186 (mt-10) REVERT: E 414 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7650 (mp10) REVERT: E 433 VAL cc_start: 0.7890 (p) cc_final: 0.7607 (m) REVERT: E 511 VAL cc_start: 0.8527 (t) cc_final: 0.8071 (m) outliers start: 11 outliers final: 9 residues processed: 142 average time/residue: 0.1448 time to fit residues: 27.0776 Evaluate side-chains 145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 15 optimal weight: 0.0020 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4982 Z= 0.181 Angle : 0.589 7.953 6785 Z= 0.301 Chirality : 0.044 0.165 742 Planarity : 0.004 0.067 874 Dihedral : 4.510 28.605 685 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 21.98 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.41 (0.34), residues: 619 helix: -3.50 (0.56), residues: 41 sheet: -0.18 (0.33), residues: 250 loop : -1.15 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 110 HIS 0.002 0.000 HIS A 109 PHE 0.010 0.001 PHE E 374 TYR 0.025 0.002 TYR B 140 ARG 0.001 0.000 ARG A 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.522 Fit side-chains REVERT: A 115 SER cc_start: 0.7870 (t) cc_final: 0.7345 (p) REVERT: A 142 MET cc_start: 0.7826 (mtm) cc_final: 0.7366 (mmp) REVERT: A 186 SER cc_start: 0.8571 (m) cc_final: 0.8288 (p) REVERT: B 4 MET cc_start: 0.7135 (ttt) cc_final: 0.6826 (ttt) REVERT: B 9 LYS cc_start: 0.7726 (mttt) cc_final: 0.7473 (mttt) REVERT: B 107 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8130 (mttp) REVERT: B 108 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7897 (ttt-90) REVERT: B 123 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8326 (mp0) REVERT: E 341 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8244 (t) REVERT: E 360 ASN cc_start: 0.8035 (t0) cc_final: 0.7563 (t0) REVERT: E 394 ASN cc_start: 0.8366 (p0) cc_final: 0.7898 (p0) REVERT: E 406 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7056 (mt-10) REVERT: E 433 VAL cc_start: 0.7898 (p) cc_final: 0.7643 (m) REVERT: E 511 VAL cc_start: 0.8527 (t) cc_final: 0.8062 (m) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.1412 time to fit residues: 26.6226 Evaluate side-chains 145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 33 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121594 restraints weight = 7650.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125438 restraints weight = 3835.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127892 restraints weight = 2210.792| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4982 Z= 0.170 Angle : 0.578 7.963 6785 Z= 0.296 Chirality : 0.043 0.161 742 Planarity : 0.004 0.066 874 Dihedral : 4.435 26.501 685 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.47 % Allowed : 23.44 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.35 (0.34), residues: 619 helix: -3.33 (0.59), residues: 40 sheet: -0.27 (0.34), residues: 243 loop : -1.01 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.001 0.000 HIS A 109 PHE 0.008 0.001 PHE E 347 TYR 0.025 0.002 TYR B 140 ARG 0.001 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1436.00 seconds wall clock time: 26 minutes 55.44 seconds (1615.44 seconds total)