Starting phenix.real_space_refine on Thu Jun 5 02:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zb9_39898/06_2025/8zb9_39898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zb9_39898/06_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_39898/06_2025/8zb9_39898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zb9_39898/06_2025/8zb9_39898.map" model { file = "/net/cci-nas-00/data/ceres_data/8zb9_39898/06_2025/8zb9_39898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zb9_39898/06_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-5710/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: 3.88, per 1000 atoms: 0.79 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: 1.12 Conformation dependent library (CDL) restraints added in 588.7 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: 0.58 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: 1.22 Time building geometry restraints manager: 1.37 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- 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 : 0.569 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: 0.1484 time to fit residues: 17.8371 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 : 0.579 ------------------------------------------------------------------------------- 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: 0.3491 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.592 Fit side-chains REVERT: a 208 ASN cc_start: 0.7791 (t0) cc_final: 0.7189 (t0) outliers start: 19 outliers final: 12 residues processed: 92 average time/residue: 0.1698 time to fit residues: 20.3495 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 : 0.567 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138897 restraints weight = 5322.467| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.88 r_work: 0.3427 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1372 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= 0.220 Angle : 0.668 7.315 6821 Z= 0.352 Chirality : 0.047 0.142 698 Planarity : 0.005 0.056 889 Dihedral : 5.138 22.421 664 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 5.16 % Allowed : 21.92 % 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: -2.72 (0.33), residues: 604 helix: 1.40 (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 0.03859 ( 110) hydrogen bonds : angle 4.72186 ( 303) SS BOND : bond 0.00344 ( 11) SS BOND : angle 1.52773 ( 22) covalent geometry : bond 0.00520 ( 5031) covalent geometry : angle 0.66329 ( 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 111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 ASN cc_start: 0.7833 (t0) cc_final: 0.7200 (t0) outliers start: 28 outliers final: 20 residues processed: 103 average time/residue: 0.1369 time to fit residues: 18.9671 Evaluate side-chains 95 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 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 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: 1.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.182896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146724 restraints weight = 5294.493| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.89 r_work: 0.3530 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1877 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= 0.110 Angle : 0.565 7.066 6821 Z= 0.294 Chirality : 0.044 0.141 698 Planarity : 0.005 0.055 889 Dihedral : 4.600 21.696 664 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.24 % Allowed : 24.13 % Favored : 71.64 % 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: 1.61 (0.62), residues: 72 sheet: -2.04 (0.54), residues: 95 loop : -2.20 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.002 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 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 110) hydrogen bonds : angle 4.20794 ( 303) SS BOND : bond 0.00319 ( 11) SS BOND : angle 1.17881 ( 22) covalent geometry : bond 0.00270 ( 5031) covalent geometry : angle 0.56167 ( 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 107 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8203 (tp30) cc_final: 0.7928 (tp30) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.1523 time to fit residues: 20.3955 Evaluate side-chains 93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142705 restraints weight = 5382.142| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.90 r_work: 0.3455 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5042 Z= 0.167 Angle : 0.609 7.414 6821 Z= 0.318 Chirality : 0.045 0.137 698 Planarity : 0.005 0.056 889 Dihedral : 4.729 21.347 664 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % 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: -2.40 (0.34), residues: 604 helix: 1.54 (0.62), residues: 72 sheet: -1.92 (0.54), residues: 95 loop : -2.24 (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 323 TYR 0.006 0.001 TYR A 221 ARG 0.004 0.000 ARG a 69 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 110) hydrogen bonds : angle 4.24001 ( 303) SS BOND : bond 0.00340 ( 11) SS BOND : angle 1.32440 ( 22) covalent geometry : bond 0.00397 ( 5031) covalent geometry : angle 0.60526 ( 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 109 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7729 (mt-10) REVERT: a 66 GLU cc_start: 0.8283 (tp30) cc_final: 0.8081 (tp30) outliers start: 30 outliers final: 25 residues processed: 102 average time/residue: 0.1499 time to fit residues: 20.4858 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 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 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 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: 1.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.183534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147509 restraints weight = 5266.937| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.82 r_work: 0.3518 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2094 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= 0.107 Angle : 0.553 7.898 6821 Z= 0.287 Chirality : 0.043 0.131 698 Planarity : 0.005 0.056 889 Dihedral : 4.355 21.024 664 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.16 % Allowed : 25.60 % Favored : 69.24 % 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: -2.25 (0.34), residues: 604 helix: 1.60 (0.61), residues: 72 sheet: -1.76 (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 0.002 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 0.02553 ( 110) hydrogen bonds : angle 3.93828 ( 303) SS BOND : bond 0.00305 ( 11) SS BOND : angle 1.13128 ( 22) covalent geometry : bond 0.00265 ( 5031) covalent geometry : angle 0.55058 ( 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 108 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 101 average time/residue: 0.1373 time to fit residues: 18.8403 Evaluate side-chains 94 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 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 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 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: 0.9980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.180076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144755 restraints weight = 5222.210| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.61 r_work: 0.3504 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5042 Z= 0.140 Angle : 0.591 7.644 6821 Z= 0.308 Chirality : 0.044 0.134 698 Planarity : 0.005 0.055 889 Dihedral : 4.400 20.454 664 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 5.34 % Allowed : 26.15 % 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: -2.24 (0.34), residues: 604 helix: 1.54 (0.61), residues: 72 sheet: -1.71 (0.54), 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 0.004 0.001 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 314 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 110) hydrogen bonds : angle 4.00478 ( 303) SS BOND : bond 0.00416 ( 11) SS BOND : angle 1.38268 ( 22) covalent geometry : bond 0.00340 ( 5031) covalent geometry : angle 0.58659 ( 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 109 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7714 (mt-10) REVERT: a 2 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7805 (mp10) outliers start: 29 outliers final: 27 residues processed: 103 average time/residue: 0.1526 time to fit residues: 21.1623 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 : 0.552 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144688 restraints weight = 5381.254| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.69 r_work: 0.3504 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5042 Z= 0.155 Angle : 0.616 10.137 6821 Z= 0.318 Chirality : 0.045 0.131 698 Planarity : 0.005 0.054 889 Dihedral : 4.524 20.563 664 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 6.45 % Allowed : 25.60 % Favored : 67.96 % 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: -2.25 (0.34), residues: 604 helix: 1.44 (0.61), residues: 73 sheet: -1.73 (0.54), residues: 95 loop : -2.13 (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 0.010 0.001 PHE A 104 TYR 0.006 0.001 TYR A 221 ARG 0.002 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 110) hydrogen bonds : angle 4.07563 ( 303) SS BOND : bond 0.00328 ( 11) SS BOND : angle 1.17845 ( 22) covalent geometry : bond 0.00370 ( 5031) covalent geometry : angle 0.61295 ( 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 111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7717 (mt-10) outliers start: 35 outliers final: 29 residues processed: 104 average time/residue: 0.1320 time to fit residues: 18.7704 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 : 0.582 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.176641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141514 restraints weight = 5277.412| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.74 r_work: 0.3457 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5042 Z= 0.184 Angle : 0.640 9.320 6821 Z= 0.332 Chirality : 0.046 0.133 698 Planarity : 0.005 0.054 889 Dihedral : 4.717 21.014 664 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 5.89 % Allowed : 25.97 % Favored : 68.14 % 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: -2.33 (0.34), residues: 604 helix: 1.48 (0.60), residues: 73 sheet: -1.83 (0.54), residues: 95 loop : -2.18 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.006 0.001 HIS a 205 PHE 0.011 0.001 PHE A 323 TYR 0.007 0.001 TYR a 32 ARG 0.002 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 110) hydrogen bonds : angle 4.16279 ( 303) SS BOND : bond 0.00445 ( 11) SS BOND : angle 1.45480 ( 22) covalent geometry : bond 0.00438 ( 5031) covalent geometry : angle 0.63567 ( 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 107 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7744 (mt-10) REVERT: a 2 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7835 (mp10) outliers start: 32 outliers final: 28 residues processed: 99 average time/residue: 0.1699 time to fit residues: 23.2510 Evaluate side-chains 102 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 87 SER 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: 0.3980 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN a 91 GLN ** a 255 ASN ** 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 = 0.4076 r_free = 0.4076 target = 0.180111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143434 restraints weight = 5273.793| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.90 r_work: 0.3481 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5042 Z= 0.130 Angle : 0.597 8.644 6821 Z= 0.309 Chirality : 0.044 0.158 698 Planarity : 0.005 0.054 889 Dihedral : 4.486 21.011 664 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.97 % Allowed : 27.26 % Favored : 67.77 % 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: 1.75 (0.60), residues: 72 sheet: -1.77 (0.54), residues: 95 loop : -2.15 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.003 0.001 HIS a 205 PHE 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 221 ARG 0.001 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 110) hydrogen bonds : angle 3.99161 ( 303) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.12412 ( 22) covalent geometry : bond 0.00316 ( 5031) covalent geometry : angle 0.59414 ( 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 : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7708 (mt-10) REVERT: a 2 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7830 (mp10) outliers start: 27 outliers final: 27 residues processed: 99 average time/residue: 0.1446 time to fit residues: 19.8348 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 : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 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 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 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 A 154 GLN ** a 255 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.180017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143823 restraints weight = 5276.746| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.87 r_work: 0.3491 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2272 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 : 0.597 8.590 6821 Z= 0.309 Chirality : 0.044 0.147 698 Planarity : 0.005 0.054 889 Dihedral : 4.421 20.809 664 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 4.60 % Allowed : 27.62 % Favored : 67.77 % 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: -2.17 (0.34), residues: 604 helix: 1.82 (0.59), residues: 72 sheet: -1.72 (0.54), residues: 95 loop : -2.11 (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 0.010 0.001 PHE A 104 TYR 0.005 0.001 TYR A 221 ARG 0.001 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 110) hydrogen bonds : angle 3.96161 ( 303) SS BOND : bond 0.00371 ( 11) SS BOND : angle 1.34705 ( 22) covalent geometry : bond 0.00319 ( 5031) covalent geometry : angle 0.59289 ( 6799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.08 seconds wall clock time: 50 minutes 10.52 seconds (3010.52 seconds total)