Starting phenix.real_space_refine on Wed Mar 5 15:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5d_36902/03_2025/8k5d_36902.cif" } resolution = 3.74 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= -0.001 sd= 0.031 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 17 5.16 5 Cl 1 4.86 5 C 1561 2.51 5 N 394 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2345 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2328 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.96 Number of scatterers: 2345 At special positions: 0 Unit cell: (69.72, 62.25, 79.68, 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) Cl 1 17.00 S 17 16.00 O 372 8.00 N 394 7.00 C 1561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 0.64 Conformation dependent library (CDL) restraints added in 266.7 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 75.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 166 removed outlier: 5.124A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.816A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 260 removed outlier: 3.717A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.597A pdb=" N ARG A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 165 hydrogen bonds defined for protein. 483 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: 0.66 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 713 1.34 - 1.46: 438 1.46 - 1.58: 1236 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 2413 Sorted by residual: bond pdb=" C07 OKL A 401 " pdb=" O08 OKL A 401 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C10 OKL A 401 " pdb=" O11 OKL A 401 " ideal model delta sigma weight residual 1.215 1.396 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C15 OKL A 401 " pdb="CL17 OKL A 401 " ideal model delta sigma weight residual 1.692 1.784 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.390 1.325 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.384 1.328 0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 2408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3204 1.90 - 3.81: 50 3.81 - 5.71: 22 5.71 - 7.62: 4 7.62 - 9.52: 4 Bond angle restraints: 3284 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.91 108.72 3.19 8.90e-01 1.26e+00 1.28e+01 angle pdb=" N PRO A 31 " pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CA PRO A 31 " pdb=" C PRO A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 117.93 121.72 -3.79 1.20e+00 6.94e-01 9.98e+00 angle pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " pdb=" C10 OKL A 401 " ideal model delta sigma weight residual 129.77 120.31 9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C12 OKL A 401 " pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 109.84 119.23 -9.39 3.00e+00 1.11e-01 9.80e+00 ... (remaining 3279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 1261 27.19 - 54.38: 120 54.38 - 81.58: 7 81.58 - 108.77: 0 108.77 - 135.96: 1 Dihedral angle restraints: 1389 sinusoidal: 535 harmonic: 854 Sorted by residual: dihedral pdb=" C03 OKL A 401 " pdb=" C04 OKL A 401 " pdb=" C05 OKL A 401 " pdb=" N06 OKL A 401 " ideal model delta sinusoidal sigma weight residual 183.45 47.49 135.96 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA LYS A 164 " pdb=" C LYS A 164 " pdb=" N LYS A 165 " pdb=" CA LYS A 165 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU A 196 " pdb=" C GLU A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 261 0.037 - 0.074: 82 0.074 - 0.110: 28 0.110 - 0.147: 4 0.147 - 0.184: 3 Chirality restraints: 378 Sorted by residual: chirality pdb=" CA ASN A 110 " pdb=" N ASN A 110 " pdb=" C ASN A 110 " pdb=" CB ASN A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA THR A 159 " pdb=" N THR A 159 " pdb=" C THR A 159 " pdb=" CB THR A 159 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 375 not shown) Planarity restraints: 398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 167 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 168 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 32 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 131 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.022 5.00e-02 4.00e+02 ... (remaining 395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 258 2.74 - 3.28: 2460 3.28 - 3.82: 3903 3.82 - 4.36: 4195 4.36 - 4.90: 7307 Nonbonded interactions: 18123 Sorted by model distance: nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 68 " pdb=" NE1 TRP A 152 " model vdw 2.322 3.120 nonbonded pdb=" N SER A 179 " pdb=" O08 OKL A 401 " model vdw 2.326 3.120 nonbonded pdb=" NH2 ARG A 111 " pdb=" O11 OKL A 401 " model vdw 2.330 3.120 nonbonded pdb=" N ASP A 221 " pdb=" OD1 ASP A 221 " model vdw 2.345 3.120 ... (remaining 18118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.184 2413 Z= 0.474 Angle : 0.756 9.520 3284 Z= 0.371 Chirality : 0.043 0.184 378 Planarity : 0.005 0.045 398 Dihedral : 19.082 135.960 825 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.40 % Allowed : 41.70 % Favored : 57.89 % 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: 0.46 (0.51), residues: 289 helix: 1.39 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -2.40 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4006 (OUTLIER) cc_final: 0.3713 (m-10) REVERT: A 103 MET cc_start: 0.7450 (tpp) cc_final: 0.7040 (tpp) REVERT: A 170 GLN cc_start: 0.8195 (tp40) cc_final: 0.7866 (tp40) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0887 time to fit residues: 7.9859 Evaluate side-chains 68 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.150502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133180 restraints weight = 3897.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136323 restraints weight = 2306.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138564 restraints weight = 1581.915| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.215 Angle : 0.582 7.377 3284 Z= 0.302 Chirality : 0.040 0.136 378 Planarity : 0.005 0.048 398 Dihedral : 9.573 141.875 319 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.07 % Allowed : 33.60 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.50), residues: 289 helix: 1.21 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.68 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.009 0.001 TYR A 284 ARG 0.001 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8478 (m-80) cc_final: 0.8268 (m-80) REVERT: A 290 ASP cc_start: 0.8576 (m-30) cc_final: 0.8278 (m-30) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.0950 time to fit residues: 8.9553 Evaluate side-chains 78 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.152550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135122 restraints weight = 3897.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138160 restraints weight = 2359.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140391 restraints weight = 1657.268| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2413 Z= 0.256 Angle : 0.599 8.146 3284 Z= 0.307 Chirality : 0.040 0.132 378 Planarity : 0.005 0.050 398 Dihedral : 9.239 143.668 317 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.88 % Allowed : 32.79 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.51), residues: 289 helix: 1.35 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -2.66 (0.68), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.003 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.002 TYR A 284 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8542 (m-80) cc_final: 0.8231 (m-80) REVERT: A 103 MET cc_start: 0.7686 (tpp) cc_final: 0.7452 (tpp) REVERT: A 290 ASP cc_start: 0.8667 (m-30) cc_final: 0.8188 (m-30) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.1062 time to fit residues: 9.9951 Evaluate side-chains 79 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.151228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133983 restraints weight = 3864.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136985 restraints weight = 2334.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139117 restraints weight = 1628.531| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2413 Z= 0.271 Angle : 0.604 6.569 3284 Z= 0.311 Chirality : 0.041 0.131 378 Planarity : 0.005 0.048 398 Dihedral : 9.267 143.530 317 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 8.91 % Allowed : 31.17 % Favored : 59.92 % 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: 0.51 (0.51), residues: 289 helix: 1.38 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.71 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.002 TYR A 284 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3875 (OUTLIER) cc_final: 0.3607 (m-10) REVERT: A 110 ASN cc_start: 0.8548 (m-40) cc_final: 0.8273 (m110) REVERT: A 290 ASP cc_start: 0.8698 (m-30) cc_final: 0.8046 (m-30) outliers start: 22 outliers final: 17 residues processed: 78 average time/residue: 0.1005 time to fit residues: 9.7202 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.0020 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.153040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135530 restraints weight = 3947.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138663 restraints weight = 2329.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140933 restraints weight = 1605.101| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.217 Angle : 0.581 8.684 3284 Z= 0.297 Chirality : 0.040 0.133 378 Planarity : 0.005 0.049 398 Dihedral : 9.125 141.626 317 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 8.10 % Allowed : 32.39 % Favored : 59.51 % 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: 0.65 (0.51), residues: 289 helix: 1.61 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.92 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.006 0.001 TYR A 126 ARG 0.001 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3856 (OUTLIER) cc_final: 0.3630 (m-10) REVERT: A 63 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8187 (ttm-80) REVERT: A 282 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (t80) REVERT: A 290 ASP cc_start: 0.8688 (m-30) cc_final: 0.8345 (m-30) outliers start: 20 outliers final: 16 residues processed: 76 average time/residue: 0.1124 time to fit residues: 10.6807 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.153071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135302 restraints weight = 3817.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138533 restraints weight = 2279.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140658 restraints weight = 1579.277| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2413 Z= 0.218 Angle : 0.612 8.987 3284 Z= 0.312 Chirality : 0.041 0.155 378 Planarity : 0.005 0.050 398 Dihedral : 9.123 141.437 317 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 8.91 % Allowed : 32.39 % Favored : 58.70 % 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: 0.62 (0.51), residues: 289 helix: 1.40 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.62 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.007 0.001 TYR A 284 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3839 (OUTLIER) cc_final: 0.3615 (m-10) REVERT: A 63 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8187 (ttm-80) REVERT: A 110 ASN cc_start: 0.8671 (m-40) cc_final: 0.8460 (m110) REVERT: A 290 ASP cc_start: 0.8726 (m-30) cc_final: 0.8365 (m-30) outliers start: 22 outliers final: 17 residues processed: 80 average time/residue: 0.1093 time to fit residues: 10.9233 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129761 restraints weight = 3998.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132742 restraints weight = 2403.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135081 restraints weight = 1679.921| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2413 Z= 0.364 Angle : 0.681 8.699 3284 Z= 0.348 Chirality : 0.043 0.143 378 Planarity : 0.005 0.047 398 Dihedral : 9.495 146.669 317 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 9.31 % Allowed : 31.98 % Favored : 58.70 % 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: 0.27 (0.50), residues: 289 helix: 1.20 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.80 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.002 0.001 HIS A 184 PHE 0.009 0.001 PHE A 206 TYR 0.013 0.002 TYR A 126 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3954 (OUTLIER) cc_final: 0.3722 (m-10) REVERT: A 110 ASN cc_start: 0.8668 (m-40) cc_final: 0.8392 (m110) REVERT: A 290 ASP cc_start: 0.8736 (m-30) cc_final: 0.8330 (m-30) outliers start: 23 outliers final: 20 residues processed: 78 average time/residue: 0.1052 time to fit residues: 10.1861 Evaluate side-chains 87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.151500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133781 restraints weight = 4011.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136796 restraints weight = 2387.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138974 restraints weight = 1655.900| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2413 Z= 0.228 Angle : 0.629 8.883 3284 Z= 0.317 Chirality : 0.041 0.137 378 Planarity : 0.005 0.048 398 Dihedral : 9.183 141.484 317 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.69 % Allowed : 33.20 % Favored : 59.11 % 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: 0.47 (0.51), residues: 289 helix: 1.51 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.03 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 54 TYR 0.006 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3883 (OUTLIER) cc_final: 0.3650 (m-10) REVERT: A 63 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.8185 (ttm-80) REVERT: A 110 ASN cc_start: 0.8691 (m-40) cc_final: 0.8459 (m110) REVERT: A 190 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9023 (mm-30) REVERT: A 290 ASP cc_start: 0.8697 (m-30) cc_final: 0.8279 (m-30) outliers start: 19 outliers final: 16 residues processed: 76 average time/residue: 0.1106 time to fit residues: 10.4796 Evaluate side-chains 83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 25 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 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 = 0.3786 r_free = 0.3786 target = 0.156142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138640 restraints weight = 3852.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141775 restraints weight = 2283.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144148 restraints weight = 1579.085| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2413 Z= 0.179 Angle : 0.596 8.943 3284 Z= 0.299 Chirality : 0.040 0.134 378 Planarity : 0.005 0.051 398 Dihedral : 8.760 135.179 317 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.45 % Allowed : 36.44 % Favored : 59.11 % 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: 0.73 (0.52), residues: 289 helix: 1.52 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.67 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 91 HIS 0.002 0.000 HIS A 161 PHE 0.014 0.001 PHE A 197 TYR 0.004 0.001 TYR A 295 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7921 (mt-10) REVERT: A 110 ASN cc_start: 0.8665 (m-40) cc_final: 0.8396 (m110) REVERT: A 137 ASN cc_start: 0.8214 (m-40) cc_final: 0.7797 (m-40) REVERT: A 290 ASP cc_start: 0.8571 (m-30) cc_final: 0.8034 (m-30) outliers start: 11 outliers final: 11 residues processed: 78 average time/residue: 0.1097 time to fit residues: 10.6116 Evaluate side-chains 78 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 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 = 0.3762 r_free = 0.3762 target = 0.153915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136227 restraints weight = 3921.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139365 restraints weight = 2316.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141730 restraints weight = 1590.757| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2413 Z= 0.213 Angle : 0.612 8.995 3284 Z= 0.307 Chirality : 0.040 0.135 378 Planarity : 0.005 0.051 398 Dihedral : 8.899 137.796 317 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.26 % Allowed : 34.82 % Favored : 59.92 % 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: 0.69 (0.51), residues: 289 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.72 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.000 HIS A 161 PHE 0.012 0.001 PHE A 197 TYR 0.006 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8696 (m-40) cc_final: 0.8339 (m110) REVERT: A 137 ASN cc_start: 0.8319 (m-40) cc_final: 0.7831 (m-40) REVERT: A 190 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8924 (mm-30) REVERT: A 290 ASP cc_start: 0.8635 (m-30) cc_final: 0.8205 (m-30) outliers start: 13 outliers final: 13 residues processed: 75 average time/residue: 0.1057 time to fit residues: 9.8121 Evaluate side-chains 80 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134275 restraints weight = 3953.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137388 restraints weight = 2349.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139443 restraints weight = 1616.728| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2413 Z= 0.266 Angle : 0.637 8.729 3284 Z= 0.322 Chirality : 0.041 0.137 378 Planarity : 0.005 0.050 398 Dihedral : 9.165 142.187 317 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.07 % Allowed : 34.41 % Favored : 59.51 % 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: 0.55 (0.51), residues: 289 helix: 1.57 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.06 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.001 0.001 HIS A 161 PHE 0.011 0.001 PHE A 54 TYR 0.010 0.002 TYR A 126 ARG 0.003 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1093.93 seconds wall clock time: 19 minutes 44.40 seconds (1184.40 seconds total)