Starting phenix.real_space_refine on Thu Mar 6 04:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zb9_39898/03_2025/8zb9_39898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zb9_39898/03_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_39898/03_2025/8zb9_39898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zb9_39898/03_2025/8zb9_39898.map" model { file = "/net/cci-nas-00/data/ceres_data/8zb9_39898/03_2025/8zb9_39898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zb9_39898/03_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-5624/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: 3.70, per 1000 atoms: 0.75 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: 1.19 Conformation dependent library (CDL) restraints added in 603.1 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: 0.59 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: 1.21 Time building geometry restraints manager: 1.43 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: 3.670 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: 0.040 Set scattering table: 0.050 Process input model: 16.190 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- 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 : 0.534 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: 0.1462 time to fit residues: 17.5494 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 : 0.559 ------------------------------------------------------------------------------- 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: 0.3497 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.586 Fit side-chains REVERT: a 208 ASN cc_start: 0.7782 (t0) cc_final: 0.7164 (t0) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 0.1638 time to fit residues: 19.5479 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 : 0.611 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.184579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147428 restraints weight = 5273.342| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.95 r_work: 0.3508 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5031 Z= 0.185 Angle : 0.559 7.133 6799 Z= 0.292 Chirality : 0.044 0.139 698 Planarity : 0.005 0.053 889 Dihedral : 4.544 22.264 664 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.24 % Allowed : 22.84 % Favored : 72.93 % 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: -2.41 (0.34), residues: 604 helix: 1.64 (0.62), residues: 72 sheet: -2.13 (0.54), residues: 95 loop : -2.21 (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 109 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8009 (tt0) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 0.1463 time to fit residues: 20.0929 Evaluate side-chains 89 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 58 optimal weight: 0.0000 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.185437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148095 restraints weight = 5338.058| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.96 r_work: 0.3512 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5031 Z= 0.184 Angle : 0.552 7.164 6799 Z= 0.286 Chirality : 0.043 0.131 698 Planarity : 0.005 0.053 889 Dihedral : 4.372 21.416 664 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % 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: -2.28 (0.34), residues: 604 helix: 1.66 (0.61), residues: 72 sheet: -2.03 (0.54), residues: 95 loop : -2.11 (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 260 ARG 0.001 0.000 ARG a 338 *********************** 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 104 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7987 (tt0) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 0.1317 time to fit residues: 17.4610 Evaluate side-chains 90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.180344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144782 restraints weight = 5330.812| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.72 r_work: 0.3491 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1837 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= 0.249 Angle : 0.588 6.483 6799 Z= 0.306 Chirality : 0.044 0.131 698 Planarity : 0.005 0.054 889 Dihedral : 4.555 21.281 664 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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: 1.72 (0.62), residues: 72 sheet: -1.87 (0.55), residues: 95 loop : -2.12 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.005 0.001 HIS a 256 PHE 0.011 0.001 PHE A 104 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG a 166 *********************** 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 : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7842 (mp10) outliers start: 29 outliers final: 25 residues processed: 103 average time/residue: 0.1413 time to fit residues: 19.6347 Evaluate side-chains 101 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.5980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.181467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144934 restraints weight = 5277.176| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.87 r_work: 0.3488 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2007 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= 0.206 Angle : 0.579 7.599 6799 Z= 0.301 Chirality : 0.044 0.130 698 Planarity : 0.005 0.054 889 Dihedral : 4.403 21.241 664 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 6.08 % Allowed : 23.57 % 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: -2.19 (0.34), residues: 604 helix: 1.75 (0.61), residues: 72 sheet: -1.78 (0.55), residues: 95 loop : -2.10 (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 0.006 0.001 TYR A 35 ARG 0.002 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 113 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 27 residues processed: 104 average time/residue: 0.1650 time to fit residues: 22.8327 Evaluate side-chains 101 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.178171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142818 restraints weight = 5233.953| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.56 r_work: 0.3492 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5031 Z= 0.285 Angle : 0.623 9.329 6799 Z= 0.323 Chirality : 0.045 0.133 698 Planarity : 0.005 0.055 889 Dihedral : 4.612 20.877 664 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 6.26 % Allowed : 24.13 % Favored : 69.61 % 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: -2.28 (0.34), residues: 604 helix: 1.61 (0.61), residues: 72 sheet: -1.77 (0.54), residues: 95 loop : -2.17 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.005 0.001 HIS a 205 PHE 0.011 0.001 PHE A 104 TYR 0.006 0.001 TYR a 32 ARG 0.002 0.000 ARG a 314 *********************** 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 112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7847 (mp10) outliers start: 34 outliers final: 30 residues processed: 104 average time/residue: 0.1968 time to fit residues: 28.3676 Evaluate side-chains 103 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 84 VAL 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 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 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 321 VAL 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: 0.7980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.178747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142546 restraints weight = 5339.193| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.83 r_work: 0.3493 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5031 Z= 0.261 Angle : 0.614 7.822 6799 Z= 0.320 Chirality : 0.045 0.140 698 Planarity : 0.005 0.056 889 Dihedral : 4.608 21.164 664 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 5.52 % Allowed : 24.68 % 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: -2.29 (0.34), residues: 604 helix: 1.52 (0.60), residues: 73 sheet: -1.78 (0.54), residues: 95 loop : -2.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.005 0.001 HIS a 205 PHE 0.011 0.001 PHE A 104 TYR 0.006 0.001 TYR A 221 ARG 0.002 0.000 ARG a 166 *********************** 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 106 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7911 (mp10) outliers start: 30 outliers final: 29 residues processed: 99 average time/residue: 0.1389 time to fit residues: 18.6476 Evaluate side-chains 100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 297 SER 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 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 321 VAL 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: 5.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.174100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138278 restraints weight = 5312.536| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.79 r_work: 0.3424 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5031 Z= 0.411 Angle : 0.694 7.761 6799 Z= 0.364 Chirality : 0.048 0.152 698 Planarity : 0.005 0.055 889 Dihedral : 5.056 21.468 664 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % 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: -2.45 (0.33), residues: 604 helix: 1.45 (0.61), residues: 72 sheet: -1.76 (0.55), residues: 93 loop : -2.32 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 226 HIS 0.008 0.002 HIS a 205 PHE 0.014 0.002 PHE A 323 TYR 0.009 0.001 TYR a 32 ARG 0.003 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 106 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (mtmm) REVERT: a 2 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7999 (mp10) REVERT: a 177 ILE cc_start: 0.9021 (pt) cc_final: 0.8817 (mt) REVERT: a 326 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8129 (p) outliers start: 30 outliers final: 25 residues processed: 98 average time/residue: 0.1688 time to fit residues: 22.5473 Evaluate side-chains 100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 192 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 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 SER 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 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 321 VAL Chi-restraints excluded: chain a residue 326 SER 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: 0.0980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146061 restraints weight = 5269.967| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.85 r_work: 0.3522 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5031 Z= 0.191 Angle : 0.584 8.210 6799 Z= 0.303 Chirality : 0.043 0.133 698 Planarity : 0.005 0.056 889 Dihedral : 4.421 21.488 664 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.24 % Allowed : 26.70 % Favored : 69.06 % 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: 1.54 (0.59), residues: 73 sheet: -1.74 (0.54), residues: 95 loop : -2.13 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.002 0.000 HIS A 205 PHE 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 221 ARG 0.001 0.000 ARG a 336 ********************** 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 100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7844 (mp10) outliers start: 23 outliers final: 20 residues processed: 94 average time/residue: 0.2686 time to fit residues: 33.4875 Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 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 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 19 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 50 optimal weight: 0.3980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147868 restraints weight = 5251.176| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.85 r_work: 0.3546 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5031 Z= 0.188 Angle : 0.569 8.940 6799 Z= 0.293 Chirality : 0.043 0.124 698 Planarity : 0.005 0.056 889 Dihedral : 4.159 20.641 664 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.87 % Allowed : 27.26 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.34), residues: 604 helix: 1.86 (0.60), residues: 73 sheet: -1.65 (0.54), residues: 97 loop : -2.00 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 201 HIS 0.002 0.001 HIS a 205 PHE 0.009 0.001 PHE A 104 TYR 0.004 0.001 TYR A 221 ARG 0.004 0.000 ARG a 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.94 seconds wall clock time: 50 minutes 22.65 seconds (3022.65 seconds total)