Starting phenix.real_space_refine on Sat Jun 14 06:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902.map" model { file = "/net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu1_21902/06_2025/6wu1_21902_neut_trim.cif" } resolution = 3.09 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= 1.000 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5222 2.51 5 N 1176 2.21 5 O 1260 1.98 5 H 7826 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15534 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7673 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "B" Number of atoms: 7673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7673 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 110 Unusual residues: {'D10': 5, 'HEX': 6, 'OCT': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 78 Unusual residues: {'D10': 3, 'HEX': 4, 'OCT': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 8.06, per 1000 atoms: 0.52 Number of scatterers: 15534 At special positions: 0 Unit cell: (78.6, 103.752, 77.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1260 8.00 N 1176 7.00 C 5222 6.00 H 7826 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 80.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 34 through 54 Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.568A pdb=" N THR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.613A pdb=" N ARG A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 removed outlier: 4.030A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 181 through 186 removed outlier: 4.051A pdb=" N LYS A 185 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.803A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 removed outlier: 5.148A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 280 through 300 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 358 removed outlier: 3.954A pdb=" N TRP A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.661A pdb=" N VAL A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.900A pdb=" N MET A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 455 through 485 Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.568A pdb=" N THR B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.613A pdb=" N ARG B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.029A pdb=" N ALA B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 181 through 186 removed outlier: 4.050A pdb=" N LYS B 185 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 186 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.803A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 255 removed outlier: 5.147A pdb=" N VAL B 238 " --> pdb=" O TRP B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 280 through 300 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 358 removed outlier: 3.954A pdb=" N TRP B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.900A pdb=" N MET B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 442 through 449 Processing helix chain 'B' and resid 455 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 540 hydrogen bonds defined for protein. 1590 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: 5.72 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7822 1.03 - 1.22: 4 1.22 - 1.42: 3154 1.42 - 1.61: 4648 1.61 - 1.81: 96 Bond restraints: 15724 Sorted by residual: bond pdb=" N ALA A 0 " pdb=" CA ALA A 0 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.58e+00 bond pdb=" N ALA B 0 " pdb=" CA ALA B 0 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.45e+00 bond pdb=" N ALA B 0 " pdb=" H ALA B 0 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" N ALA A 0 " pdb=" H ALA A 0 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 HEX A 513 " pdb=" C2 HEX A 513 " ideal model delta sigma weight residual 1.523 1.494 0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 15719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.40: 28446 7.40 - 14.79: 1 14.79 - 22.19: 0 22.19 - 29.59: 0 29.59 - 36.99: 3 Bond angle restraints: 28450 Sorted by residual: angle pdb=" C ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 109.00 72.01 36.99 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 110.00 73.68 36.32 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CB ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 109.00 75.92 33.08 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N THR A 438 " pdb=" CA THR A 438 " pdb=" C THR A 438 " ideal model delta sigma weight residual 108.34 112.90 -4.56 1.31e+00 5.83e-01 1.21e+01 angle pdb=" N THR B 438 " pdb=" CA THR B 438 " pdb=" C THR B 438 " ideal model delta sigma weight residual 108.34 112.84 -4.50 1.31e+00 5.83e-01 1.18e+01 ... (remaining 28445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6340 17.41 - 34.82: 698 34.82 - 52.22: 266 52.22 - 69.63: 90 69.63 - 87.04: 10 Dihedral angle restraints: 7404 sinusoidal: 3964 harmonic: 3440 Sorted by residual: dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ILE A 485 " pdb=" C ILE A 485 " pdb=" N GLY A 486 " pdb=" CA GLY A 486 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 735 0.032 - 0.064: 352 0.064 - 0.097: 116 0.097 - 0.129: 35 0.129 - 0.161: 4 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ALA B 0 " pdb=" N ALA B 0 " pdb=" C ALA B 0 " pdb=" CB ALA B 0 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ALA A 0 " pdb=" N ALA A 0 " pdb=" C ALA A 0 " pdb=" CB ALA A 0 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE A 375 " pdb=" N ILE A 375 " pdb=" C ILE A 375 " pdb=" CB ILE A 375 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1239 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 165 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 166 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 165 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 166 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 181 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO A 182 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.018 5.00e-02 4.00e+02 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 171 2.05 - 2.69: 24416 2.69 - 3.33: 46808 3.33 - 3.96: 58846 3.96 - 4.60: 96149 Nonbonded interactions: 226390 Sorted by model distance: nonbonded pdb=" O ARG B 134 " pdb=" H GLY B 137 " model vdw 1.416 2.450 nonbonded pdb=" O ARG A 134 " pdb=" H GLY A 137 " model vdw 1.416 2.450 nonbonded pdb=" H ALA B 0 " pdb=" HA ALA B 0 " model vdw 1.576 1.816 nonbonded pdb=" O GLY B 65 " pdb=" HG1 THR B 69 " model vdw 1.623 2.450 nonbonded pdb=" O GLY A 65 " pdb=" HG1 THR A 69 " model vdw 1.627 2.450 ... (remaining 226385 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 0 through 488 or resid 502 or resid 506 through 507)) selection = (chain 'B' and (resid 0 through 488 or resid 502 or resid 506 through 507)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.510 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: 0.250 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.140 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7898 Z= 0.275 Angle : 0.780 7.434 10690 Z= 0.380 Chirality : 0.042 0.161 1242 Planarity : 0.004 0.037 1254 Dihedral : 15.684 85.294 2766 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.44 % Favored : 94.15 % Rotamer: Outliers : 2.78 % Allowed : 15.19 % Favored : 82.03 % 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: -2.60 (0.24), residues: 974 helix: -1.26 (0.17), residues: 742 sheet: None (None), residues: 0 loop : -2.73 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 344 HIS 0.006 0.002 HIS A 197 PHE 0.009 0.001 PHE B 464 TYR 0.008 0.001 TYR B 252 ARG 0.001 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.12241 ( 540) hydrogen bonds : angle 5.86251 ( 1590) covalent geometry : bond 0.00680 ( 7898) covalent geometry : angle 0.77974 (10690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.037 Fit side-chains REVERT: A 131 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 253 LYS cc_start: 0.7526 (tptm) cc_final: 0.7126 (tttm) REVERT: B 131 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 253 LYS cc_start: 0.7911 (tptm) cc_final: 0.7361 (tttm) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.3648 time to fit residues: 50.2283 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN ** B 392 HIS ** 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 = 0.3565 r_free = 0.3565 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117760 restraints weight = 25049.998| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.89 r_work: 0.3290 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7898 Z= 0.172 Angle : 0.584 10.455 10690 Z= 0.313 Chirality : 0.042 0.416 1242 Planarity : 0.005 0.044 1254 Dihedral : 8.279 57.573 1160 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.57 % Favored : 93.22 % Rotamer: Outliers : 2.78 % Allowed : 15.82 % Favored : 81.39 % 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: -0.59 (0.27), residues: 974 helix: 0.16 (0.18), residues: 744 sheet: None (None), residues: 0 loop : -1.95 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 344 HIS 0.006 0.001 HIS A 334 PHE 0.012 0.001 PHE A 474 TYR 0.015 0.001 TYR A 255 ARG 0.002 0.000 ARG B 159 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 540) hydrogen bonds : angle 4.89537 ( 1590) covalent geometry : bond 0.00403 ( 7898) covalent geometry : angle 0.58353 (10690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.190 Fit side-chains REVERT: A 5 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: A 131 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7059 (p90) REVERT: A 253 LYS cc_start: 0.7974 (tptm) cc_final: 0.7334 (tttm) REVERT: B 131 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7056 (p90) REVERT: B 219 MET cc_start: 0.8264 (mmm) cc_final: 0.7340 (mmt) REVERT: B 253 LYS cc_start: 0.8365 (tptm) cc_final: 0.7612 (tttm) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 0.3660 time to fit residues: 56.2893 Evaluate side-chains 100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119947 restraints weight = 26483.258| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.82 r_work: 0.3379 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7898 Z= 0.154 Angle : 0.536 10.272 10690 Z= 0.287 Chirality : 0.042 0.412 1242 Planarity : 0.005 0.043 1254 Dihedral : 7.630 59.848 1151 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 1.52 % Allowed : 16.71 % Favored : 81.77 % 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: 0.19 (0.28), residues: 974 helix: 0.72 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.73 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.005 0.001 HIS A 197 PHE 0.011 0.001 PHE A 474 TYR 0.014 0.001 TYR A 255 ARG 0.001 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 540) hydrogen bonds : angle 4.70128 ( 1590) covalent geometry : bond 0.00355 ( 7898) covalent geometry : angle 0.53553 (10690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.114 Fit side-chains REVERT: A 5 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 131 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7106 (p90) REVERT: A 253 LYS cc_start: 0.8439 (tptm) cc_final: 0.7799 (tttm) REVERT: A 462 MET cc_start: 0.8439 (mtm) cc_final: 0.8209 (mtm) REVERT: A 482 MET cc_start: 0.6893 (mtt) cc_final: 0.6414 (mtt) REVERT: B 131 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7091 (p90) REVERT: B 219 MET cc_start: 0.8370 (mmm) cc_final: 0.7500 (mmt) REVERT: B 253 LYS cc_start: 0.8571 (tptm) cc_final: 0.7857 (tttm) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.3690 time to fit residues: 56.1586 Evaluate side-chains 97 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 271 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120867 restraints weight = 26471.964| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.82 r_work: 0.3389 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7898 Z= 0.113 Angle : 0.506 10.473 10690 Z= 0.270 Chirality : 0.041 0.431 1242 Planarity : 0.005 0.042 1254 Dihedral : 7.050 59.250 1146 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.54 % Favored : 94.25 % Rotamer: Outliers : 2.41 % Allowed : 16.84 % Favored : 80.76 % 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: 0.61 (0.28), residues: 974 helix: 1.03 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.62 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.004 0.001 HIS A 197 PHE 0.010 0.001 PHE B 474 TYR 0.010 0.001 TYR A 255 ARG 0.001 0.000 ARG B 159 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 540) hydrogen bonds : angle 4.53744 ( 1590) covalent geometry : bond 0.00246 ( 7898) covalent geometry : angle 0.50588 (10690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.054 Fit side-chains REVERT: A 5 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7935 (mt-10) REVERT: A 131 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6884 (p90) REVERT: A 253 LYS cc_start: 0.8479 (tptm) cc_final: 0.7806 (tttm) REVERT: B 131 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6905 (p90) REVERT: B 253 LYS cc_start: 0.8515 (tptm) cc_final: 0.7819 (tttm) outliers start: 19 outliers final: 3 residues processed: 102 average time/residue: 0.3756 time to fit residues: 54.3801 Evaluate side-chains 87 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN B 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117029 restraints weight = 27396.156| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.85 r_work: 0.3339 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7898 Z= 0.157 Angle : 0.536 10.378 10690 Z= 0.287 Chirality : 0.042 0.430 1242 Planarity : 0.006 0.045 1254 Dihedral : 6.866 57.960 1138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 1.14 % Allowed : 18.10 % Favored : 80.76 % 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: 0.71 (0.28), residues: 974 helix: 1.08 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.50 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.005 0.001 HIS B 197 PHE 0.011 0.001 PHE B 474 TYR 0.012 0.001 TYR A 255 ARG 0.001 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 540) hydrogen bonds : angle 4.60226 ( 1590) covalent geometry : bond 0.00367 ( 7898) covalent geometry : angle 0.53590 (10690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.207 Fit side-chains REVERT: A 131 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7017 (p90) REVERT: A 253 LYS cc_start: 0.8585 (tptm) cc_final: 0.7878 (tttm) REVERT: B 1 MET cc_start: 0.7593 (ttt) cc_final: 0.7309 (ttt) REVERT: B 131 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7060 (p90) REVERT: B 253 LYS cc_start: 0.8569 (tptm) cc_final: 0.7865 (tttm) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.3748 time to fit residues: 49.7684 Evaluate side-chains 90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122228 restraints weight = 27066.415| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.85 r_work: 0.3351 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7898 Z= 0.126 Angle : 0.511 10.435 10690 Z= 0.272 Chirality : 0.041 0.430 1242 Planarity : 0.005 0.044 1254 Dihedral : 6.200 54.670 1136 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.65 % Allowed : 18.23 % Favored : 80.13 % 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: 0.88 (0.28), residues: 974 helix: 1.20 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.44 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.005 0.001 HIS B 197 PHE 0.010 0.001 PHE B 474 TYR 0.009 0.001 TYR A 255 ARG 0.001 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 540) hydrogen bonds : angle 4.48848 ( 1590) covalent geometry : bond 0.00286 ( 7898) covalent geometry : angle 0.51056 (10690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.133 Fit side-chains REVERT: A 131 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6854 (p90) REVERT: A 253 LYS cc_start: 0.8562 (tptm) cc_final: 0.7857 (tttm) REVERT: A 462 MET cc_start: 0.8446 (mtm) cc_final: 0.8197 (mtm) REVERT: B 1 MET cc_start: 0.7682 (ttt) cc_final: 0.7434 (ttt) REVERT: B 131 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.6955 (p90) REVERT: B 219 MET cc_start: 0.8471 (mmm) cc_final: 0.7844 (mmt) REVERT: B 253 LYS cc_start: 0.8612 (tptm) cc_final: 0.7894 (tttm) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.3833 time to fit residues: 52.9273 Evaluate side-chains 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106114 restraints weight = 27306.883| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.08 r_work: 0.3182 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7898 Z= 0.134 Angle : 0.516 10.449 10690 Z= 0.276 Chirality : 0.041 0.431 1242 Planarity : 0.005 0.044 1254 Dihedral : 6.034 55.586 1136 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 1.39 % Allowed : 18.73 % Favored : 79.87 % 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: 0.98 (0.28), residues: 974 helix: 1.27 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 344 HIS 0.004 0.001 HIS B 197 PHE 0.009 0.001 PHE B 474 TYR 0.009 0.001 TYR A 255 ARG 0.001 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 540) hydrogen bonds : angle 4.49975 ( 1590) covalent geometry : bond 0.00307 ( 7898) covalent geometry : angle 0.51629 (10690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.109 Fit side-chains REVERT: A 131 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6797 (p90) REVERT: A 253 LYS cc_start: 0.8506 (tptm) cc_final: 0.7726 (tttm) REVERT: A 462 MET cc_start: 0.8456 (mtm) cc_final: 0.8211 (mtm) REVERT: B 131 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.6788 (p90) REVERT: B 219 MET cc_start: 0.8280 (mmm) cc_final: 0.7675 (mmt) REVERT: B 253 LYS cc_start: 0.8532 (tptm) cc_final: 0.7755 (tttm) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.4003 time to fit residues: 53.4230 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106786 restraints weight = 27188.397| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.07 r_work: 0.3190 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7898 Z= 0.120 Angle : 0.507 10.443 10690 Z= 0.269 Chirality : 0.041 0.431 1242 Planarity : 0.005 0.044 1254 Dihedral : 5.793 53.242 1136 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.54 % Favored : 94.25 % Rotamer: Outliers : 1.65 % Allowed : 18.99 % Favored : 79.37 % 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: 1.11 (0.28), residues: 974 helix: 1.36 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.35 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.004 0.001 HIS B 197 PHE 0.008 0.001 PHE B 474 TYR 0.008 0.001 TYR A 255 ARG 0.001 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 540) hydrogen bonds : angle 4.42667 ( 1590) covalent geometry : bond 0.00268 ( 7898) covalent geometry : angle 0.50738 (10690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.199 Fit side-chains REVERT: A 131 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.6626 (p90) REVERT: A 253 LYS cc_start: 0.8492 (tptm) cc_final: 0.7727 (tttm) REVERT: A 462 MET cc_start: 0.8457 (mtm) cc_final: 0.8194 (mtm) REVERT: B 131 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6683 (p90) REVERT: B 219 MET cc_start: 0.8279 (mmm) cc_final: 0.7675 (mmt) REVERT: B 253 LYS cc_start: 0.8522 (tptm) cc_final: 0.7751 (tttm) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.3756 time to fit residues: 53.7787 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110006 restraints weight = 27039.915| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.07 r_work: 0.3182 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7898 Z= 0.109 Angle : 0.502 10.457 10690 Z= 0.266 Chirality : 0.040 0.431 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.630 53.924 1136 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 1.39 % Allowed : 19.87 % Favored : 78.73 % 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: 1.21 (0.28), residues: 974 helix: 1.43 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS A 334 PHE 0.008 0.001 PHE B 474 TYR 0.007 0.001 TYR A 255 ARG 0.001 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 540) hydrogen bonds : angle 4.39493 ( 1590) covalent geometry : bond 0.00240 ( 7898) covalent geometry : angle 0.50211 (10690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.212 Fit side-chains REVERT: A 131 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6617 (p90) REVERT: A 253 LYS cc_start: 0.8496 (tptm) cc_final: 0.7742 (tttm) REVERT: A 462 MET cc_start: 0.8447 (mtm) cc_final: 0.8191 (mtm) REVERT: B 131 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6764 (p90) REVERT: B 219 MET cc_start: 0.8297 (mmm) cc_final: 0.7633 (mmt) REVERT: B 253 LYS cc_start: 0.8484 (tptm) cc_final: 0.7745 (tttm) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.3820 time to fit residues: 52.3636 Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105847 restraints weight = 27607.884| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.10 r_work: 0.3205 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7898 Z= 0.106 Angle : 0.496 10.464 10690 Z= 0.262 Chirality : 0.040 0.431 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.415 51.177 1136 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 1.27 % Allowed : 19.87 % Favored : 78.86 % 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: 1.36 (0.28), residues: 974 helix: 1.55 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS B 197 PHE 0.007 0.001 PHE B 474 TYR 0.008 0.001 TYR A 255 ARG 0.001 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 540) hydrogen bonds : angle 4.31861 ( 1590) covalent geometry : bond 0.00234 ( 7898) covalent geometry : angle 0.49626 (10690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.189 Fit side-chains REVERT: A 131 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6537 (p90) REVERT: A 253 LYS cc_start: 0.8489 (tptm) cc_final: 0.7725 (tttm) REVERT: A 462 MET cc_start: 0.8422 (mtm) cc_final: 0.8146 (mtm) REVERT: B 131 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6593 (p90) REVERT: B 219 MET cc_start: 0.8282 (mmm) cc_final: 0.7608 (mmt) REVERT: B 253 LYS cc_start: 0.8487 (tptm) cc_final: 0.7761 (tttm) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.3794 time to fit residues: 52.8513 Evaluate side-chains 97 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106196 restraints weight = 27467.979| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.09 r_work: 0.3192 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7898 Z= 0.105 Angle : 0.497 10.475 10690 Z= 0.262 Chirality : 0.040 0.431 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.398 52.214 1136 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 1.27 % Allowed : 19.62 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.28), residues: 974 helix: 1.62 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS A 334 PHE 0.007 0.001 PHE B 474 TYR 0.007 0.001 TYR A 255 ARG 0.001 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 540) hydrogen bonds : angle 4.30972 ( 1590) covalent geometry : bond 0.00230 ( 7898) covalent geometry : angle 0.49662 (10690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7010.76 seconds wall clock time: 120 minutes 6.67 seconds (7206.67 seconds total)