Starting phenix.real_space_refine on Thu Jun 5 01:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9f_32366/06_2025/7w9f_32366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9f_32366/06_2025/7w9f_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_32366/06_2025/7w9f_32366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9f_32366/06_2025/7w9f_32366.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9f_32366/06_2025/7w9f_32366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9f_32366/06_2025/7w9f_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-5710/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: 3.30, per 1000 atoms: 0.68 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: 1.06 Conformation dependent library (CDL) restraints added in 561.0 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: 0.68 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: 1.34 Time building geometry restraints manager: 1.27 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: 0.290 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.350 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- 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 4990 Z= 0.164 Angle : 0.729 10.679 6801 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 Details of bonding type rmsd hydrogen bonds : bond 0.30562 ( 119) hydrogen bonds : angle 10.48149 ( 303) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.74746 ( 16) covalent geometry : bond 0.00340 ( 4982) covalent geometry : angle 0.72876 ( 6785) *********************** 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 : 0.548 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: 0.1672 time to fit residues: 29.3439 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 : 0.534 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121971 restraints weight = 7658.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125916 restraints weight = 3788.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128380 restraints weight = 2142.711| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 4990 Z= 0.182 Angle : 0.585 6.935 6801 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 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 119) hydrogen bonds : angle 7.24812 ( 303) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.78112 ( 16) covalent geometry : bond 0.00402 ( 4982) covalent geometry : angle 0.58427 ( 6785) *********************** 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 : 0.529 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.6316 (ttm) cc_final: 0.5732 (tpp) REVERT: A 115 SER cc_start: 0.7748 (t) cc_final: 0.7249 (p) REVERT: A 129 TYR cc_start: 0.7730 (m-80) cc_final: 0.7495 (m-80) REVERT: A 186 SER cc_start: 0.8579 (m) cc_final: 0.8337 (p) REVERT: B 9 LYS cc_start: 0.7785 (mttt) cc_final: 0.7509 (mttt) REVERT: B 11 MET cc_start: 0.7742 (mtm) cc_final: 0.7513 (mtt) REVERT: B 108 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.7899 (ttt-90) REVERT: B 206 VAL cc_start: 0.7330 (t) cc_final: 0.7004 (p) REVERT: E 341 VAL cc_start: 0.8288 (m) cc_final: 0.8066 (t) REVERT: E 360 ASN cc_start: 0.7550 (t0) cc_final: 0.7228 (t0) REVERT: E 394 ASN cc_start: 0.8526 (p0) cc_final: 0.8198 (p0) REVERT: E 414 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8109 (mp10) REVERT: E 508 TYR cc_start: 0.7235 (m-80) cc_final: 0.6934 (m-80) REVERT: E 512 VAL cc_start: 0.7704 (t) cc_final: 0.7489 (p) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.1451 time to fit residues: 26.4140 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 : 0.568 ------------------------------------------------------------------------------- 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 38 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 48 optimal weight: 0.0060 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122005 restraints weight = 7794.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125988 restraints weight = 3877.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128556 restraints weight = 2226.599| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4990 Z= 0.101 Angle : 0.541 6.926 6801 Z= 0.282 Chirality : 0.043 0.179 742 Planarity : 0.004 0.062 874 Dihedral : 4.178 22.805 685 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.65 % Allowed : 16.85 % Favored : 81.50 % 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: -2.20 (0.32), residues: 619 helix: -4.43 (0.34), residues: 34 sheet: -0.78 (0.31), residues: 253 loop : -1.67 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 119) hydrogen bonds : angle 6.45272 ( 303) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.63761 ( 16) covalent geometry : bond 0.00223 ( 4982) covalent geometry : angle 0.54124 ( 6785) *********************** 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 155 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7792 (t) cc_final: 0.7333 (p) REVERT: A 129 TYR cc_start: 0.7687 (m-80) cc_final: 0.7416 (m-80) REVERT: A 186 SER cc_start: 0.8505 (m) cc_final: 0.8216 (p) REVERT: B 9 LYS cc_start: 0.7703 (mttt) cc_final: 0.7448 (mttt) REVERT: B 107 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8290 (ttmm) REVERT: B 108 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7751 (ttt-90) REVERT: E 341 VAL cc_start: 0.8207 (m) cc_final: 0.7928 (t) REVERT: E 360 ASN cc_start: 0.7477 (t0) cc_final: 0.7116 (t0) REVERT: E 394 ASN cc_start: 0.8702 (p0) cc_final: 0.8259 (p0) REVERT: E 396 TYR cc_start: 0.7300 (m-80) cc_final: 0.6857 (m-80) REVERT: E 406 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7076 (mp0) REVERT: E 414 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7992 (mp10) REVERT: E 508 TYR cc_start: 0.7264 (m-80) cc_final: 0.6973 (m-80) outliers start: 9 outliers final: 8 residues processed: 150 average time/residue: 0.1578 time to fit residues: 30.3951 Evaluate side-chains 150 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121620 restraints weight = 7904.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125609 restraints weight = 3905.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128172 restraints weight = 2233.603| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4990 Z= 0.117 Angle : 0.543 7.620 6801 Z= 0.282 Chirality : 0.043 0.166 742 Planarity : 0.004 0.063 874 Dihedral : 4.214 22.915 685 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.56 % Allowed : 17.22 % Favored : 80.22 % 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: -1.88 (0.32), residues: 619 helix: -4.07 (0.46), residues: 34 sheet: -0.57 (0.31), residues: 253 loop : -1.45 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.001 0.000 HIS E 519 PHE 0.022 0.001 PHE E 429 TYR 0.026 0.001 TYR B 140 ARG 0.005 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 119) hydrogen bonds : angle 6.13223 ( 303) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.80827 ( 16) covalent geometry : bond 0.00263 ( 4982) covalent geometry : angle 0.54236 ( 6785) *********************** 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 147 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7840 (t) cc_final: 0.7331 (p) REVERT: A 129 TYR cc_start: 0.7739 (m-80) cc_final: 0.7483 (m-80) REVERT: A 186 SER cc_start: 0.8517 (m) cc_final: 0.8223 (p) REVERT: B 9 LYS cc_start: 0.7725 (mttt) cc_final: 0.7461 (mttt) REVERT: B 107 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8221 (mttp) REVERT: B 108 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7973 (ttt-90) REVERT: E 341 VAL cc_start: 0.8267 (m) cc_final: 0.7983 (t) REVERT: E 360 ASN cc_start: 0.7687 (t0) cc_final: 0.7311 (t0) REVERT: E 396 TYR cc_start: 0.7268 (m-80) cc_final: 0.6883 (m-10) REVERT: E 398 ASP cc_start: 0.6560 (m-30) cc_final: 0.6200 (m-30) REVERT: E 414 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8055 (mp10) REVERT: E 508 TYR cc_start: 0.7274 (m-80) cc_final: 0.6954 (m-80) REVERT: E 511 VAL cc_start: 0.8389 (t) cc_final: 0.8154 (m) outliers start: 14 outliers final: 12 residues processed: 138 average time/residue: 0.1466 time to fit residues: 26.7461 Evaluate side-chains 144 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 89 GLU 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 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 15 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120074 restraints weight = 7780.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124024 restraints weight = 3849.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126541 restraints weight = 2204.484| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4990 Z= 0.154 Angle : 0.565 7.087 6801 Z= 0.293 Chirality : 0.043 0.170 742 Planarity : 0.004 0.062 874 Dihedral : 4.316 25.316 685 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.93 % Allowed : 18.32 % Favored : 78.75 % 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: -1.78 (0.32), residues: 619 helix: -3.71 (0.58), residues: 33 sheet: -0.56 (0.31), residues: 254 loop : -1.37 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.002 0.000 HIS E 519 PHE 0.009 0.001 PHE E 400 TYR 0.025 0.002 TYR B 140 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 119) hydrogen bonds : angle 6.00403 ( 303) SS BOND : bond 0.00251 ( 8) SS BOND : angle 0.93987 ( 16) covalent geometry : bond 0.00343 ( 4982) covalent geometry : angle 0.56399 ( 6785) *********************** 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 150 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7861 (t) cc_final: 0.7351 (p) REVERT: A 129 TYR cc_start: 0.7839 (m-80) cc_final: 0.7577 (m-80) REVERT: A 186 SER cc_start: 0.8568 (m) cc_final: 0.8213 (p) REVERT: B 9 LYS cc_start: 0.7746 (mttt) cc_final: 0.7485 (mttt) REVERT: B 107 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8242 (mttp) REVERT: B 108 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7962 (ttt-90) REVERT: B 175 MET cc_start: 0.7466 (ttp) cc_final: 0.7140 (ttt) REVERT: E 341 VAL cc_start: 0.8413 (m) cc_final: 0.8149 (t) REVERT: E 360 ASN cc_start: 0.7810 (t0) cc_final: 0.7403 (t0) REVERT: E 365 TYR cc_start: 0.8057 (m-10) cc_final: 0.7703 (m-10) REVERT: E 398 ASP cc_start: 0.6528 (m-30) cc_final: 0.6240 (m-30) REVERT: E 433 VAL cc_start: 0.7976 (p) cc_final: 0.7626 (m) REVERT: E 508 TYR cc_start: 0.7241 (m-80) cc_final: 0.6945 (m-80) REVERT: E 511 VAL cc_start: 0.8491 (t) cc_final: 0.8091 (m) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.1490 time to fit residues: 27.7740 Evaluate side-chains 145 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 7 SER 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 Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 0.0020 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118370 restraints weight = 7827.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122292 restraints weight = 3878.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124797 restraints weight = 2218.765| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4990 Z= 0.194 Angle : 0.595 7.011 6801 Z= 0.308 Chirality : 0.044 0.174 742 Planarity : 0.004 0.067 874 Dihedral : 4.567 27.190 685 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.56 % Allowed : 18.68 % Favored : 78.75 % 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: -1.68 (0.32), residues: 619 helix: -3.43 (0.65), residues: 34 sheet: -0.43 (0.32), residues: 251 loop : -1.38 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 436 HIS 0.002 0.001 HIS A 109 PHE 0.017 0.001 PHE E 429 TYR 0.027 0.002 TYR B 140 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 119) hydrogen bonds : angle 5.96617 ( 303) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.00081 ( 16) covalent geometry : bond 0.00432 ( 4982) covalent geometry : angle 0.59381 ( 6785) *********************** 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 152 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7880 (t) cc_final: 0.7361 (p) REVERT: A 129 TYR cc_start: 0.7855 (m-80) cc_final: 0.7605 (m-80) REVERT: A 186 SER cc_start: 0.8673 (m) cc_final: 0.8298 (p) REVERT: B 9 LYS cc_start: 0.7766 (mttt) cc_final: 0.7508 (mttt) REVERT: B 108 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7961 (ttt-90) REVERT: B 123 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8326 (mp0) REVERT: B 206 VAL cc_start: 0.7320 (t) cc_final: 0.7030 (p) REVERT: E 341 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8207 (t) REVERT: E 360 ASN cc_start: 0.7876 (t0) cc_final: 0.7445 (t0) REVERT: E 398 ASP cc_start: 0.6520 (m-30) cc_final: 0.6235 (m-30) REVERT: E 414 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8042 (mp10) REVERT: E 433 VAL cc_start: 0.8000 (p) cc_final: 0.7639 (m) REVERT: E 508 TYR cc_start: 0.7202 (m-80) cc_final: 0.6960 (m-80) REVERT: E 511 VAL cc_start: 0.8595 (t) cc_final: 0.8153 (m) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.1442 time to fit residues: 26.8718 Evaluate side-chains 146 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 104 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120007 restraints weight = 7716.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123957 restraints weight = 3844.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126424 restraints weight = 2195.323| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4990 Z= 0.123 Angle : 0.558 6.714 6801 Z= 0.289 Chirality : 0.043 0.166 742 Planarity : 0.004 0.066 874 Dihedral : 4.347 22.632 685 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.83 % Allowed : 20.70 % 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: -1.49 (0.33), residues: 619 helix: -3.35 (0.67), residues: 34 sheet: -0.30 (0.32), residues: 250 loop : -1.24 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.001 0.000 HIS E 519 PHE 0.019 0.001 PHE E 429 TYR 0.028 0.002 TYR B 140 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 119) hydrogen bonds : angle 5.72157 ( 303) SS BOND : bond 0.00315 ( 8) SS BOND : angle 0.80975 ( 16) covalent geometry : bond 0.00276 ( 4982) covalent geometry : angle 0.55772 ( 6785) *********************** 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 148 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7870 (t) cc_final: 0.7364 (p) REVERT: A 129 TYR cc_start: 0.7832 (m-80) cc_final: 0.7592 (m-80) REVERT: A 186 SER cc_start: 0.8610 (m) cc_final: 0.8303 (p) REVERT: B 9 LYS cc_start: 0.7748 (mttt) cc_final: 0.7510 (mttt) REVERT: B 108 ARG cc_start: 0.8155 (ttt-90) cc_final: 0.7908 (ttt-90) REVERT: B 123 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8290 (mp0) REVERT: E 341 VAL cc_start: 0.8437 (m) cc_final: 0.8190 (t) REVERT: E 360 ASN cc_start: 0.7798 (t0) cc_final: 0.7350 (t0) REVERT: E 398 ASP cc_start: 0.6510 (m-30) cc_final: 0.6247 (m-30) REVERT: E 406 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7235 (mt-10) REVERT: E 414 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7970 (mp10) REVERT: E 433 VAL cc_start: 0.7945 (p) cc_final: 0.7629 (m) REVERT: E 508 TYR cc_start: 0.7192 (m-80) cc_final: 0.6970 (m-80) REVERT: E 511 VAL cc_start: 0.8549 (t) cc_final: 0.8138 (m) outliers start: 10 outliers final: 9 residues processed: 140 average time/residue: 0.1642 time to fit residues: 30.5120 Evaluate side-chains 146 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 104 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119165 restraints weight = 7810.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123123 restraints weight = 3855.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125631 restraints weight = 2202.755| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4990 Z= 0.153 Angle : 0.578 6.555 6801 Z= 0.298 Chirality : 0.043 0.172 742 Planarity : 0.004 0.066 874 Dihedral : 4.428 24.613 685 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.20 % Allowed : 20.33 % 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: -1.39 (0.33), residues: 619 helix: -3.23 (0.70), residues: 34 sheet: -0.25 (0.33), residues: 250 loop : -1.17 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.002 0.000 HIS E 519 PHE 0.021 0.001 PHE E 429 TYR 0.030 0.002 TYR B 140 ARG 0.008 0.000 ARG E 357 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 119) hydrogen bonds : angle 5.70184 ( 303) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.79587 ( 16) covalent geometry : bond 0.00343 ( 4982) covalent geometry : angle 0.57775 ( 6785) *********************** 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 149 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 115 SER cc_start: 0.7881 (t) cc_final: 0.7359 (p) REVERT: A 186 SER cc_start: 0.8584 (m) cc_final: 0.8285 (p) REVERT: B 9 LYS cc_start: 0.7765 (mttt) cc_final: 0.7537 (mttt) REVERT: B 108 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7994 (ttt-90) REVERT: B 123 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8311 (mp0) REVERT: E 341 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (t) REVERT: E 360 ASN cc_start: 0.7851 (t0) cc_final: 0.7410 (t0) REVERT: E 398 ASP cc_start: 0.6553 (m-30) cc_final: 0.6326 (m-30) REVERT: E 406 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7262 (mt-10) REVERT: E 414 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7969 (mp10) REVERT: E 433 VAL cc_start: 0.7948 (p) cc_final: 0.7661 (m) REVERT: E 508 TYR cc_start: 0.7178 (m-80) cc_final: 0.6952 (m-80) REVERT: E 511 VAL cc_start: 0.8594 (t) cc_final: 0.8160 (m) outliers start: 12 outliers final: 8 residues processed: 141 average time/residue: 0.1884 time to fit residues: 35.5717 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 : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 104 LEU Chi-restraints excluded: chain B residue 176 SER 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 59 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120611 restraints weight = 7710.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124580 restraints weight = 3845.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127114 restraints weight = 2207.178| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4990 Z= 0.112 Angle : 0.556 6.853 6801 Z= 0.286 Chirality : 0.043 0.164 742 Planarity : 0.004 0.066 874 Dihedral : 4.247 20.906 685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.83 % Allowed : 20.70 % 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: -1.30 (0.34), residues: 619 helix: -3.26 (0.67), residues: 34 sheet: -0.21 (0.33), residues: 250 loop : -1.07 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 110 HIS 0.001 0.000 HIS E 519 PHE 0.022 0.001 PHE E 429 TYR 0.027 0.001 TYR B 140 ARG 0.006 0.000 ARG E 357 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 119) hydrogen bonds : angle 5.53236 ( 303) SS BOND : bond 0.00375 ( 8) SS BOND : angle 0.60088 ( 16) covalent geometry : bond 0.00250 ( 4982) covalent geometry : angle 0.55609 ( 6785) *********************** 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 151 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.496 Fit side-chains REVERT: A 110 TRP cc_start: 0.7670 (m100) cc_final: 0.7156 (m100) REVERT: A 115 SER cc_start: 0.7867 (t) cc_final: 0.7368 (p) REVERT: A 131 LEU cc_start: 0.8032 (tp) cc_final: 0.7817 (tp) REVERT: A 186 SER cc_start: 0.8484 (m) cc_final: 0.8220 (p) REVERT: B 9 LYS cc_start: 0.7735 (mttt) cc_final: 0.7497 (mttt) REVERT: B 108 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7992 (ttt-90) REVERT: B 123 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8298 (mp0) REVERT: E 341 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8206 (t) REVERT: E 360 ASN cc_start: 0.7847 (t0) cc_final: 0.7413 (t0) REVERT: E 394 ASN cc_start: 0.8643 (p0) cc_final: 0.8105 (p0) REVERT: E 398 ASP cc_start: 0.6522 (m-30) cc_final: 0.6261 (m-30) REVERT: E 406 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7262 (mt-10) REVERT: E 414 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7940 (mp10) REVERT: E 433 VAL cc_start: 0.7901 (p) cc_final: 0.7628 (m) REVERT: E 505 TYR cc_start: 0.7522 (t80) cc_final: 0.7270 (t80) REVERT: E 508 TYR cc_start: 0.7212 (m-80) cc_final: 0.6971 (m-80) REVERT: E 511 VAL cc_start: 0.8521 (t) cc_final: 0.8102 (m) outliers start: 10 outliers final: 9 residues processed: 144 average time/residue: 0.1362 time to fit residues: 25.8934 Evaluate side-chains 148 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 104 LEU 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 25 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.132785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120258 restraints weight = 7757.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124233 restraints weight = 3878.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126748 restraints weight = 2223.086| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4990 Z= 0.124 Angle : 0.569 7.105 6801 Z= 0.291 Chirality : 0.043 0.167 742 Planarity : 0.004 0.065 874 Dihedral : 4.282 21.903 685 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.01 % Allowed : 20.88 % 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: -1.32 (0.33), residues: 619 helix: -3.35 (0.58), residues: 40 sheet: -0.14 (0.33), residues: 249 loop : -1.10 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 110 HIS 0.001 0.000 HIS E 519 PHE 0.008 0.001 PHE E 400 TYR 0.026 0.001 TYR B 140 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 119) hydrogen bonds : angle 5.50262 ( 303) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.70017 ( 16) covalent geometry : bond 0.00278 ( 4982) covalent geometry : angle 0.56838 ( 6785) ********************** 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 150 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7702 (m100) cc_final: 0.7329 (m100) REVERT: A 115 SER cc_start: 0.7731 (t) cc_final: 0.7243 (p) REVERT: A 131 LEU cc_start: 0.8039 (tp) cc_final: 0.7829 (tp) REVERT: A 186 SER cc_start: 0.8603 (m) cc_final: 0.8319 (p) REVERT: B 9 LYS cc_start: 0.7751 (mttt) cc_final: 0.7524 (mttt) REVERT: B 108 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7983 (ttt-90) REVERT: B 123 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8271 (mp0) REVERT: E 341 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8212 (t) REVERT: E 360 ASN cc_start: 0.7860 (t0) cc_final: 0.7435 (t0) REVERT: E 394 ASN cc_start: 0.8651 (p0) cc_final: 0.8217 (p0) REVERT: E 406 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 414 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7955 (mp10) REVERT: E 433 VAL cc_start: 0.7939 (p) cc_final: 0.7682 (m) REVERT: E 505 TYR cc_start: 0.7547 (t80) cc_final: 0.7302 (t80) REVERT: E 508 TYR cc_start: 0.7208 (m-80) cc_final: 0.6899 (m-80) REVERT: E 511 VAL cc_start: 0.8548 (t) cc_final: 0.8122 (m) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 0.1463 time to fit residues: 27.4650 Evaluate side-chains 146 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 104 LEU 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 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120380 restraints weight = 7784.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124339 restraints weight = 3866.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126847 restraints weight = 2220.932| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4990 Z= 0.121 Angle : 0.581 7.164 6801 Z= 0.299 Chirality : 0.044 0.209 742 Planarity : 0.004 0.065 874 Dihedral : 4.475 31.564 685 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.65 % Allowed : 22.16 % 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: -1.31 (0.33), residues: 619 helix: -3.37 (0.58), residues: 41 sheet: -0.10 (0.33), residues: 249 loop : -1.10 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 110 HIS 0.001 0.000 HIS E 519 PHE 0.009 0.001 PHE E 429 TYR 0.029 0.001 TYR B 140 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 119) hydrogen bonds : angle 5.44186 ( 303) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.17591 ( 16) covalent geometry : bond 0.00272 ( 4982) covalent geometry : angle 0.57931 ( 6785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.11 seconds wall clock time: 37 minutes 25.91 seconds (2245.91 seconds total)