Starting phenix.real_space_refine on Sat May 10 03:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zb9_39898/05_2025/8zb9_39898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zb9_39898/05_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_39898/05_2025/8zb9_39898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zb9_39898/05_2025/8zb9_39898.map" model { file = "/net/cci-nas-00/data/ceres_data/8zb9_39898/05_2025/8zb9_39898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zb9_39898/05_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-5687/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: 3.65, per 1000 atoms: 0.74 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: 1.00 Conformation dependent library (CDL) restraints added in 526.8 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: 0.57 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: 1.21 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.690 Find NCS groups from input model: 0.190 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- 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 : 0.008 0.254 5042 Z= 0.429 Angle : 1.103 49.213 6821 Z= 0.602 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 Details of bonding type rmsd hydrogen bonds : bond 0.22492 ( 110) hydrogen bonds : angle 7.49101 ( 303) SS BOND : bond 0.08155 ( 11) SS BOND : angle 11.86805 ( 22) covalent geometry : bond 0.00726 ( 5031) covalent geometry : angle 0.87422 ( 6799) *********************** 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 : 0.545 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: 0.1461 time to fit residues: 17.5889 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 : 0.581 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143714 restraints weight = 5294.028| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.86 r_work: 0.3490 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5042 Z= 0.142 Angle : 0.623 7.467 6821 Z= 0.329 Chirality : 0.046 0.197 698 Planarity : 0.005 0.055 889 Dihedral : 5.009 22.356 664 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.50 % Allowed : 22.65 % Favored : 73.85 % 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: -2.63 (0.34), residues: 604 helix: 1.44 (0.63), residues: 72 sheet: -2.02 (0.60), residues: 84 loop : -2.44 (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 260 ARG 0.002 0.000 ARG a 314 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 110) hydrogen bonds : angle 4.79391 ( 303) SS BOND : bond 0.00594 ( 11) SS BOND : angle 1.73392 ( 22) covalent geometry : bond 0.00338 ( 5031) covalent geometry : angle 0.61589 ( 6799) *********************** 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: 19 poor density : 80 time to evaluate : 0.575 Fit side-chains REVERT: a 208 ASN cc_start: 0.7787 (t0) cc_final: 0.7185 (t0) outliers start: 19 outliers final: 12 residues processed: 92 average time/residue: 0.1683 time to fit residues: 20.0600 Evaluate side-chains 90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 204 SER 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: 2.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138673 restraints weight = 5324.135| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.87 r_work: 0.3423 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5042 Z= 0.221 Angle : 0.670 7.204 6821 Z= 0.353 Chirality : 0.047 0.141 698 Planarity : 0.005 0.057 889 Dihedral : 5.157 22.667 664 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 5.34 % Allowed : 21.92 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.72 (0.33), residues: 604 helix: 1.41 (0.62), residues: 72 sheet: -2.07 (0.55), residues: 93 loop : -2.51 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.008 0.001 HIS a 205 PHE 0.014 0.002 PHE A 104 TYR 0.009 0.001 TYR A 260 ARG 0.002 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 110) hydrogen bonds : angle 4.71665 ( 303) SS BOND : bond 0.00439 ( 11) SS BOND : angle 1.56609 ( 22) covalent geometry : bond 0.00520 ( 5031) covalent geometry : angle 0.66529 ( 6799) *********************** 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 113 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 208 ASN cc_start: 0.7831 (t0) cc_final: 0.7191 (t0) outliers start: 29 outliers final: 22 residues processed: 104 average time/residue: 0.1411 time to fit residues: 19.7466 Evaluate side-chains 98 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 33 SER 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 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 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 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 321 VAL 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: 0.8980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144289 restraints weight = 5328.075| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.92 r_work: 0.3500 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5042 Z= 0.126 Angle : 0.584 7.019 6821 Z= 0.304 Chirality : 0.044 0.137 698 Planarity : 0.005 0.056 889 Dihedral : 4.736 21.890 664 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.24 % Allowed : 25.23 % Favored : 70.53 % 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 (0.34), residues: 604 helix: 1.58 (0.62), residues: 72 sheet: -2.01 (0.56), residues: 91 loop : -2.28 (0.29), residues: 441 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 0.003 0.000 ARG a 69 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 110) hydrogen bonds : angle 4.27939 ( 303) SS BOND : bond 0.00353 ( 11) SS BOND : angle 1.26708 ( 22) covalent geometry : bond 0.00305 ( 5031) covalent geometry : angle 0.58022 ( 6799) *********************** 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: 23 poor density : 83 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 100 average time/residue: 0.1521 time to fit residues: 20.1725 Evaluate side-chains 95 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 172 VAL 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 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 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: 4.9990 chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.183778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146612 restraints weight = 5351.315| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.93 r_work: 0.3508 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5042 Z= 0.116 Angle : 0.569 7.405 6821 Z= 0.296 Chirality : 0.043 0.134 698 Planarity : 0.005 0.054 889 Dihedral : 4.457 21.130 664 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % 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: -2.29 (0.34), residues: 604 helix: 1.57 (0.61), residues: 72 sheet: -1.85 (0.56), residues: 91 loop : -2.15 (0.29), residues: 441 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 0.009 0.001 PHE A 104 TYR 0.004 0.001 TYR A 221 ARG 0.002 0.000 ARG a 69 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 110) hydrogen bonds : angle 4.02818 ( 303) SS BOND : bond 0.00295 ( 11) SS BOND : angle 1.16363 ( 22) covalent geometry : bond 0.00284 ( 5031) covalent geometry : angle 0.56639 ( 6799) *********************** 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: 30 poor density : 81 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7695 (mt-10) REVERT: a 66 GLU cc_start: 0.7931 (tp30) cc_final: 0.7310 (tt0) outliers start: 30 outliers final: 23 residues processed: 104 average time/residue: 0.1565 time to fit residues: 21.7102 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 : 0.526 ------------------------------------------------------------------------------- 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 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 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 329 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144731 restraints weight = 5279.549| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.86 r_work: 0.3495 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5042 Z= 0.125 Angle : 0.565 7.811 6821 Z= 0.293 Chirality : 0.044 0.133 698 Planarity : 0.005 0.054 889 Dihedral : 4.436 20.846 664 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.89 % Allowed : 24.49 % 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: -2.23 (0.34), residues: 604 helix: 1.57 (0.61), residues: 72 sheet: -1.72 (0.56), residues: 91 loop : -2.12 (0.29), residues: 441 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 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.001 0.000 ARG a 245 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 110) hydrogen bonds : angle 3.96197 ( 303) SS BOND : bond 0.00315 ( 11) SS BOND : angle 1.21184 ( 22) covalent geometry : bond 0.00303 ( 5031) covalent geometry : angle 0.56175 ( 6799) *********************** 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 114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7786 (mp10) outliers start: 32 outliers final: 26 residues processed: 106 average time/residue: 0.1375 time to fit residues: 19.7446 Evaluate side-chains 100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 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 329 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 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 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.180949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145328 restraints weight = 5226.669| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.63 r_work: 0.3530 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5042 Z= 0.130 Angle : 0.598 9.883 6821 Z= 0.308 Chirality : 0.044 0.131 698 Planarity : 0.005 0.054 889 Dihedral : 4.383 20.508 664 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 5.89 % Allowed : 25.60 % Favored : 68.51 % 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: 1.56 (0.60), residues: 72 sheet: -1.74 (0.54), residues: 95 loop : -2.09 (0.29), residues: 437 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 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.002 0.000 ARG a 314 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 110) hydrogen bonds : angle 3.98951 ( 303) SS BOND : bond 0.00415 ( 11) SS BOND : angle 1.32850 ( 22) covalent geometry : bond 0.00319 ( 5031) covalent geometry : angle 0.59392 ( 6799) *********************** 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 111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7688 (mt-10) outliers start: 32 outliers final: 28 residues processed: 104 average time/residue: 0.1300 time to fit residues: 18.4865 Evaluate side-chains 104 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 229 THR 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 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: 2.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.177740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141747 restraints weight = 5358.235| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.83 r_work: 0.3490 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5042 Z= 0.172 Angle : 0.632 8.732 6821 Z= 0.329 Chirality : 0.045 0.133 698 Planarity : 0.005 0.054 889 Dihedral : 4.623 20.541 664 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 6.45 % Allowed : 25.05 % Favored : 68.51 % 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: -2.26 (0.34), residues: 604 helix: 1.43 (0.60), residues: 73 sheet: -1.69 (0.57), residues: 91 loop : -2.14 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.006 0.001 HIS a 205 PHE 0.011 0.001 PHE A 323 TYR 0.007 0.001 TYR a 32 ARG 0.002 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 110) hydrogen bonds : angle 4.12701 ( 303) SS BOND : bond 0.00353 ( 11) SS BOND : angle 1.27333 ( 22) covalent geometry : bond 0.00409 ( 5031) covalent geometry : angle 0.62881 ( 6799) *********************** 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 109 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7680 (mt-10) outliers start: 35 outliers final: 28 residues processed: 101 average time/residue: 0.1200 time to fit residues: 16.7194 Evaluate side-chains 100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 229 THR 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 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: 2.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139950 restraints weight = 5294.857| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.71 r_work: 0.3493 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5042 Z= 0.210 Angle : 0.670 8.059 6821 Z= 0.349 Chirality : 0.046 0.137 698 Planarity : 0.005 0.054 889 Dihedral : 4.866 21.095 664 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 5.52 % Allowed : 26.15 % Favored : 68.32 % 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: -2.38 (0.34), residues: 604 helix: 1.42 (0.61), residues: 73 sheet: -1.71 (0.55), residues: 93 loop : -2.26 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.006 0.001 HIS a 256 PHE 0.012 0.001 PHE A 323 TYR 0.008 0.001 TYR a 32 ARG 0.003 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 110) hydrogen bonds : angle 4.27349 ( 303) SS BOND : bond 0.00524 ( 11) SS BOND : angle 1.52547 ( 22) covalent geometry : bond 0.00498 ( 5031) covalent geometry : angle 0.66522 ( 6799) *********************** 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 108 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7676 (mt-10) REVERT: a 2 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7784 (mp10) outliers start: 30 outliers final: 27 residues processed: 100 average time/residue: 0.1298 time to fit residues: 17.8746 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 84 VAL 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 229 THR 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 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.180922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144167 restraints weight = 5252.749| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.92 r_work: 0.3497 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5042 Z= 0.120 Angle : 0.595 8.623 6821 Z= 0.308 Chirality : 0.044 0.133 698 Planarity : 0.005 0.054 889 Dihedral : 4.435 20.965 664 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.97 % Allowed : 27.44 % Favored : 67.59 % 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: -2.22 (0.34), residues: 604 helix: 1.71 (0.59), residues: 72 sheet: -1.75 (0.54), residues: 95 loop : -2.13 (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 0.001 0.000 ARG a 336 Details of bonding type rmsd hydrogen bonds : bond 0.02591 ( 110) hydrogen bonds : angle 3.97705 ( 303) SS BOND : bond 0.00333 ( 11) SS BOND : angle 1.07403 ( 22) covalent geometry : bond 0.00295 ( 5031) covalent geometry : angle 0.59266 ( 6799) ********************** 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: 27 poor density : 78 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7706 (mt-10) REVERT: a 2 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7780 (mp10) outliers start: 27 outliers final: 25 residues processed: 99 average time/residue: 0.1289 time to fit residues: 17.4357 Evaluate side-chains 102 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 229 THR 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 104 PHE Chi-restraints excluded: chain a residue 132 SER 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 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: 0.0070 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.180867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144781 restraints weight = 5262.797| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.87 r_work: 0.3519 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5042 Z= 0.122 Angle : 0.604 8.602 6821 Z= 0.311 Chirality : 0.044 0.130 698 Planarity : 0.005 0.054 889 Dihedral : 4.345 20.599 664 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 4.42 % Allowed : 28.18 % Favored : 67.40 % 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: -2.11 (0.34), residues: 604 helix: 1.80 (0.59), residues: 72 sheet: -1.68 (0.54), residues: 95 loop : -2.05 (0.30), 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 0.001 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 110) hydrogen bonds : angle 3.92862 ( 303) SS BOND : bond 0.00465 ( 11) SS BOND : angle 1.19897 ( 22) covalent geometry : bond 0.00304 ( 5031) covalent geometry : angle 0.60063 ( 6799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.02 seconds wall clock time: 45 minutes 49.43 seconds (2749.43 seconds total)