Starting phenix.real_space_refine on Tue Jan 14 01:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.map" model { file = "/net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zb9_39898/01_2025/8zb9_39898.cif" } resolution = 3.31 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= -0.000 sd= 0.039 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 42 5.16 5 C 3075 2.51 5 N 848 2.21 5 O 939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4904 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2455 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain breaks: 4 Chain: "a" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2449 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain breaks: 3 Time building chain proxies: 3.73, per 1000 atoms: 0.76 Number of scatterers: 4904 At special positions: 0 Unit cell: (86.7, 103.7, 64.6, 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 42 16.00 O 939 8.00 N 848 7.00 C 3075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.28 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 224 " distance=2.04 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=1.97 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 224 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=1.97 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: 1.01 Conformation dependent library (CDL) restraints added in 556.4 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 16.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.341A pdb=" N ASP A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.814A pdb=" N ILE A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 27 Processing helix chain 'a' and resid 40 through 53 removed outlier: 3.570A pdb=" N GLY a 53 " --> pdb=" O SER a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.317A pdb=" N ASP a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE a 75 " --> pdb=" O ARG a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 184 removed outlier: 4.044A pdb=" N ILE a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU a 184 " --> pdb=" O GLY a 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 184' Processing helix chain 'a' and resid 227 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.567A pdb=" N GLU A 12 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 14 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 5 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN a 2 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.247A pdb=" N GLY A 56 " --> pdb=" O VAL A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.860A pdb=" N SER A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.569A pdb=" N LYS A 276 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 218 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 216 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG A 277 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N HIS A 214 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE A 213 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS A 205 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 192 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 185 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY a 185 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS a 192 " --> pdb=" O ASN a 189 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE a 200 " --> pdb=" O SER a 197 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP a 201 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU a 216 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY a 203 " --> pdb=" O HIS a 214 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR a 210 " --> pdb=" O VAL a 207 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU a 216 " --> pdb=" O VAL a 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA a 218 " --> pdb=" O LEU a 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 removed outlier: 3.567A pdb=" N ILE A 286 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.456A pdb=" N GLY a 56 " --> pdb=" O VAL a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'a' and resid 285 through 287 removed outlier: 3.794A pdb=" N CYS a 313 " --> pdb=" O ILE a 286 " (cutoff:3.500A) 110 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: 1.24 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 926 1.32 - 1.45: 1458 1.45 - 1.58: 2587 1.58 - 1.71: 0 1.71 - 1.85: 60 Bond restraints: 5031 Sorted by residual: bond pdb=" CA GLN a 2 " pdb=" C GLN a 2 " ideal model delta sigma weight residual 1.525 1.465 0.059 1.28e-02 6.10e+03 2.15e+01 bond pdb=" CA PRO A 93 " pdb=" C PRO A 93 " ideal model delta sigma weight residual 1.522 1.476 0.046 9.90e-03 1.02e+04 2.14e+01 bond pdb=" CA CYS a 4 " pdb=" C CYS a 4 " ideal model delta sigma weight residual 1.531 1.482 0.049 1.15e-02 7.56e+03 1.85e+01 bond pdb=" CA GLN A 91 " pdb=" C GLN A 91 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.32e-02 5.74e+03 1.67e+01 bond pdb=" C TYR A 97 " pdb=" O TYR A 97 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.24e-02 6.50e+03 1.30e+01 ... (remaining 5026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6417 1.71 - 3.43: 307 3.43 - 5.14: 60 5.14 - 6.86: 11 6.86 - 8.57: 4 Bond angle restraints: 6799 Sorted by residual: angle pdb=" N PRO A 93 " pdb=" CA PRO A 93 " pdb=" C PRO A 93 " ideal model delta sigma weight residual 110.50 101.93 8.57 1.57e+00 4.06e-01 2.98e+01 angle pdb=" C VAL A 96 " pdb=" CA VAL A 96 " pdb=" CB VAL A 96 " ideal model delta sigma weight residual 111.40 103.49 7.91 1.90e+00 2.77e-01 1.73e+01 angle pdb=" N LEU a 13 " pdb=" CA LEU a 13 " pdb=" C LEU a 13 " ideal model delta sigma weight residual 114.64 108.38 6.26 1.52e+00 4.33e-01 1.69e+01 angle pdb=" N CYS a 4 " pdb=" CA CYS a 4 " pdb=" C CYS a 4 " ideal model delta sigma weight residual 108.18 115.92 -7.74 2.01e+00 2.48e-01 1.48e+01 angle pdb=" N GLN A 98 " pdb=" CA GLN A 98 " pdb=" C GLN A 98 " ideal model delta sigma weight residual 109.94 115.97 -6.03 1.57e+00 4.06e-01 1.48e+01 ... (remaining 6794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 2511 16.98 - 33.97: 384 33.97 - 50.95: 89 50.95 - 67.93: 15 67.93 - 84.91: 9 Dihedral angle restraints: 3008 sinusoidal: 1247 harmonic: 1761 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 15 " pdb=" CB CYS A 15 " ideal model delta sinusoidal sigma weight residual 93.00 31.72 61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA ASP a 92 " pdb=" C ASP a 92 " pdb=" N PRO a 93 " pdb=" CA PRO a 93 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual 93.00 131.00 -38.00 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 3005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 382 0.035 - 0.071: 206 0.071 - 0.106: 79 0.106 - 0.142: 26 0.142 - 0.177: 5 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA GLN A 98 " pdb=" N GLN A 98 " pdb=" C GLN A 98 " pdb=" CB GLN A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA VAL a 149 " pdb=" N VAL a 149 " pdb=" C VAL a 149 " pdb=" CB VAL a 149 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL a 207 " pdb=" N VAL a 207 " pdb=" C VAL a 207 " pdb=" CB VAL a 207 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 695 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 280 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 281 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 314 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG A 314 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 315 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP a 38 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO a 39 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO a 39 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO a 39 " 0.030 5.00e-02 4.00e+02 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1354 2.79 - 3.32: 4194 3.32 - 3.85: 7481 3.85 - 4.37: 8734 4.37 - 4.90: 15828 Nonbonded interactions: 37591 Sorted by model distance: nonbonded pdb=" O LYS A 296 " pdb=" NH1 ARG A 336 " model vdw 2.267 3.120 nonbonded pdb=" O LYS a 296 " pdb=" NH1 ARG a 336 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR A 302 " pdb=" OD1 ASP A 303 " model vdw 2.301 3.040 nonbonded pdb=" O TYR a 34 " pdb=" NH1 ARG a 71 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP a 17 " pdb=" N GLY a 18 " model vdw 2.331 3.120 ... (remaining 37586 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 82 or resid 85 through 159 or resid 166 through \ 337)) selection = (chain 'a' and (resid 1 through 94 or resid 96 through 235 or resid 238 through \ 337)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.007 0.060 5031 Z= 0.491 Angle : 0.874 8.572 6799 Z= 0.510 Chirality : 0.051 0.177 698 Planarity : 0.006 0.055 889 Dihedral : 16.830 84.914 1845 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 0.37 % Allowed : 22.65 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.33), residues: 604 helix: 1.07 (0.59), residues: 71 sheet: -2.67 (0.55), residues: 89 loop : -2.68 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.009 0.002 HIS a 205 PHE 0.023 0.002 PHE A 104 TYR 0.012 0.002 TYR A 260 ARG 0.004 0.000 ARG a 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.547 Fit side-chains REVERT: a 4 CYS cc_start: 0.8501 (m) cc_final: 0.8287 (m) REVERT: a 208 ASN cc_start: 0.7951 (t0) cc_final: 0.7372 (t0) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.1476 time to fit residues: 17.7015 Evaluate side-chains 76 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.180570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144589 restraints weight = 5289.873| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.87 r_work: 0.3498 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.221 Angle : 0.609 7.489 6799 Z= 0.322 Chirality : 0.046 0.198 698 Planarity : 0.005 0.055 889 Dihedral : 4.954 22.325 664 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.31 % Allowed : 22.47 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.61 (0.34), residues: 604 helix: 1.45 (0.63), residues: 72 sheet: -2.04 (0.60), residues: 84 loop : -2.42 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS a 205 PHE 0.014 0.001 PHE A 104 TYR 0.006 0.001 TYR A 97 ARG 0.002 0.000 ARG a 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.584 Fit side-chains REVERT: a 208 ASN cc_start: 0.7786 (t0) cc_final: 0.7169 (t0) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 0.1699 time to fit residues: 20.3389 Evaluate side-chains 88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS 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 0 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** a 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.184877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147793 restraints weight = 5264.315| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.94 r_work: 0.3515 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5031 Z= 0.181 Angle : 0.556 7.135 6799 Z= 0.291 Chirality : 0.044 0.137 698 Planarity : 0.005 0.053 889 Dihedral : 4.507 22.158 664 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.42 % Allowed : 22.47 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.34), residues: 604 helix: 1.63 (0.62), residues: 72 sheet: -2.13 (0.54), residues: 95 loop : -2.20 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.003 0.001 HIS A 205 PHE 0.012 0.001 PHE A 104 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG a 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7987 (tt0) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 0.1364 time to fit residues: 19.0434 Evaluate side-chains 91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** 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 = 0.4071 r_free = 0.4071 target = 0.179428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143018 restraints weight = 5350.637| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.86 r_work: 0.3462 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5031 Z= 0.261 Angle : 0.605 7.179 6799 Z= 0.314 Chirality : 0.045 0.133 698 Planarity : 0.005 0.055 889 Dihedral : 4.696 21.563 664 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 4.42 % Allowed : 24.49 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.34), residues: 604 helix: 1.61 (0.61), residues: 72 sheet: -2.04 (0.54), residues: 95 loop : -2.21 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.005 0.001 HIS a 256 PHE 0.011 0.001 PHE A 104 TYR 0.007 0.001 TYR A 260 ARG 0.001 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 98 average time/residue: 0.1482 time to fit residues: 19.4463 Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** 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 = 0.4104 r_free = 0.4104 target = 0.183048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146660 restraints weight = 5310.825| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.87 r_work: 0.3521 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.196 Angle : 0.562 7.421 6799 Z= 0.291 Chirality : 0.043 0.133 698 Planarity : 0.005 0.055 889 Dihedral : 4.425 21.577 664 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.34 % Allowed : 23.57 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.34), residues: 604 helix: 1.76 (0.62), residues: 72 sheet: -1.84 (0.54), residues: 95 loop : -2.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.003 0.001 HIS a 205 PHE 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 221 ARG 0.002 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7648 (mt-10) REVERT: a 66 GLU cc_start: 0.8215 (tp30) cc_final: 0.7948 (tp30) outliers start: 29 outliers final: 24 residues processed: 102 average time/residue: 0.1439 time to fit residues: 19.5135 Evaluate side-chains 97 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.0030 chunk 20 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148240 restraints weight = 5273.712| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.87 r_work: 0.3541 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.178 Angle : 0.558 9.469 6799 Z= 0.289 Chirality : 0.043 0.128 698 Planarity : 0.005 0.054 889 Dihedral : 4.200 20.725 664 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.34 % Allowed : 23.76 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.34), residues: 604 helix: 1.86 (0.61), residues: 72 sheet: -1.66 (0.55), residues: 95 loop : -2.05 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.002 0.001 HIS a 205 PHE 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.004 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7718 (mp10) REVERT: a 66 GLU cc_start: 0.8268 (tp30) cc_final: 0.8062 (tp30) outliers start: 29 outliers final: 23 residues processed: 98 average time/residue: 0.1290 time to fit residues: 17.2915 Evaluate side-chains 96 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147730 restraints weight = 5203.599| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.84 r_work: 0.3532 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5031 Z= 0.207 Angle : 0.564 8.374 6799 Z= 0.292 Chirality : 0.043 0.128 698 Planarity : 0.005 0.053 889 Dihedral : 4.234 20.608 664 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.89 % Allowed : 23.76 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.34), residues: 604 helix: 1.90 (0.60), residues: 72 sheet: -1.61 (0.55), residues: 95 loop : -2.05 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.003 0.001 HIS a 205 PHE 0.011 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.002 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 71 ARG cc_start: 0.8616 (mmm160) cc_final: 0.6720 (mmm-85) outliers start: 32 outliers final: 28 residues processed: 102 average time/residue: 0.1356 time to fit residues: 19.0657 Evaluate side-chains 99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.181345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145407 restraints weight = 5338.050| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.80 r_work: 0.3518 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5031 Z= 0.228 Angle : 0.582 7.928 6799 Z= 0.301 Chirality : 0.044 0.128 698 Planarity : 0.005 0.053 889 Dihedral : 4.332 20.479 664 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.52 % Allowed : 24.49 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.34), residues: 604 helix: 1.80 (0.60), residues: 73 sheet: -1.62 (0.55), residues: 95 loop : -2.05 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.004 0.001 HIS a 205 PHE 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 35 ARG 0.001 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7694 (mt-10) outliers start: 30 outliers final: 28 residues processed: 100 average time/residue: 0.1422 time to fit residues: 19.4592 Evaluate side-chains 102 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141706 restraints weight = 5271.404| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.79 r_work: 0.3467 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5031 Z= 0.302 Angle : 0.631 7.283 6799 Z= 0.329 Chirality : 0.046 0.150 698 Planarity : 0.005 0.053 889 Dihedral : 4.671 20.951 664 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 5.34 % Allowed : 24.68 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.34), residues: 604 helix: 1.83 (0.59), residues: 72 sheet: -1.71 (0.55), residues: 95 loop : -2.15 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.006 0.001 HIS a 205 PHE 0.011 0.001 PHE A 323 TYR 0.008 0.001 TYR A 34 ARG 0.002 0.000 ARG a 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 71 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.6988 (mmm-85) REVERT: a 2 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7896 (mp10) outliers start: 29 outliers final: 26 residues processed: 97 average time/residue: 0.1537 time to fit residues: 19.9288 Evaluate side-chains 96 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.181546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145761 restraints weight = 5279.799| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.80 r_work: 0.3502 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5031 Z= 0.210 Angle : 0.587 8.768 6799 Z= 0.304 Chirality : 0.044 0.138 698 Planarity : 0.005 0.054 889 Dihedral : 4.359 20.893 664 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 5.16 % Allowed : 25.05 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.34), residues: 604 helix: 1.94 (0.59), residues: 72 sheet: -1.70 (0.55), residues: 95 loop : -2.08 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.003 0.001 HIS A 205 PHE 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 35 ARG 0.002 0.000 ARG A 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7745 (mt-10) REVERT: a 2 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7734 (mp10) outliers start: 28 outliers final: 26 residues processed: 100 average time/residue: 0.1347 time to fit residues: 18.4590 Evaluate side-chains 102 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 154 GLN a 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.183876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146951 restraints weight = 5299.438| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.92 r_work: 0.3526 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5031 Z= 0.202 Angle : 0.575 8.701 6799 Z= 0.296 Chirality : 0.043 0.137 698 Planarity : 0.005 0.053 889 Dihedral : 4.248 20.502 664 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.79 % Allowed : 25.41 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.34), residues: 604 helix: 1.90 (0.59), residues: 73 sheet: -1.65 (0.55), residues: 95 loop : -2.05 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.003 0.001 HIS a 205 PHE 0.009 0.001 PHE A 104 TYR 0.005 0.001 TYR A 35 ARG 0.001 0.000 ARG a 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.00 seconds wall clock time: 45 minutes 43.14 seconds (2743.14 seconds total)