Starting phenix.real_space_refine on Wed Jul 23 08:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5d_36902/07_2025/8k5d_36902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5d_36902/07_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_36902/07_2025/8k5d_36902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5d_36902/07_2025/8k5d_36902.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5d_36902/07_2025/8k5d_36902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5d_36902/07_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-5711/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: 2.36, per 1000 atoms: 1.01 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: 0.74 Conformation dependent library (CDL) restraints added in 260.8 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: 0.25 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: 0.64 Time building geometry restraints manager: 0.63 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: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- 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 2415 Z= 0.332 Angle : 0.755 9.520 3288 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 Details of bonding type rmsd hydrogen bonds : bond 0.12440 ( 165) hydrogen bonds : angle 5.08309 ( 483) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.34041 ( 4) covalent geometry : bond 0.00673 ( 2413) covalent geometry : angle 0.75568 ( 3284) *********************** 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 : 0.266 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: 0.0927 time to fit residues: 8.1302 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 : 0.271 ------------------------------------------------------------------------------- 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: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.151148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133963 restraints weight = 3898.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137043 restraints weight = 2301.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139110 restraints weight = 1579.245| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2415 Z= 0.133 Angle : 0.581 7.439 3288 Z= 0.301 Chirality : 0.040 0.133 378 Planarity : 0.005 0.049 398 Dihedral : 9.605 142.554 319 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.07 % Allowed : 33.20 % Favored : 60.73 % 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: 0.39 (0.50), residues: 289 helix: 1.22 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.70 (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 0.007 0.001 TYR A 284 ARG 0.001 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 165) hydrogen bonds : angle 4.20166 ( 483) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.17309 ( 4) covalent geometry : bond 0.00302 ( 2413) covalent geometry : angle 0.58098 ( 3284) *********************** 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 : 0.264 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8461 (m-80) cc_final: 0.8248 (m-80) REVERT: A 290 ASP cc_start: 0.8576 (m-30) cc_final: 0.8297 (m-30) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1049 time to fit residues: 9.8904 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 : 0.263 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 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 = 0.3751 r_free = 0.3751 target = 0.153120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135843 restraints weight = 3896.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138918 restraints weight = 2362.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141062 restraints weight = 1646.679| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2415 Z= 0.153 Angle : 0.594 8.087 3288 Z= 0.304 Chirality : 0.040 0.134 378 Planarity : 0.005 0.050 398 Dihedral : 9.210 143.110 317 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.88 % Allowed : 33.20 % 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: 0.50 (0.51), residues: 289 helix: 1.30 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.64 (0.69), residues: 74 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 0.001 TYR A 284 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 165) hydrogen bonds : angle 4.15798 ( 483) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.15622 ( 4) covalent geometry : bond 0.00361 ( 2413) covalent geometry : angle 0.59465 ( 3284) *********************** 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 : 0.247 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8520 (m-80) cc_final: 0.8196 (m-80) REVERT: A 103 MET cc_start: 0.7575 (tpp) cc_final: 0.7361 (tpp) REVERT: A 290 ASP cc_start: 0.8623 (m-30) cc_final: 0.8176 (m-30) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.1024 time to fit residues: 9.6340 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 : 0.227 ------------------------------------------------------------------------------- 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 88 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 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: 0.2980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136685 restraints weight = 3849.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139851 restraints weight = 2322.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141840 restraints weight = 1604.031| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2415 Z= 0.135 Angle : 0.572 6.818 3288 Z= 0.294 Chirality : 0.040 0.124 378 Planarity : 0.005 0.052 398 Dihedral : 9.161 142.417 317 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.88 % Allowed : 33.20 % 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: 0.62 (0.51), residues: 289 helix: 1.42 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.66 (0.68), residues: 75 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 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 284 ARG 0.001 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 165) hydrogen bonds : angle 4.03527 ( 483) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.14330 ( 4) covalent geometry : bond 0.00317 ( 2413) covalent geometry : angle 0.57275 ( 3284) *********************** 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 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.8247 (ttm-80) REVERT: A 290 ASP cc_start: 0.8682 (m-30) cc_final: 0.8074 (m-30) outliers start: 17 outliers final: 11 residues processed: 75 average time/residue: 0.1054 time to fit residues: 9.8353 Evaluate side-chains 77 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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=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: 0.7980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137488 restraints weight = 3927.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140580 restraints weight = 2338.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142810 restraints weight = 1617.587| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2415 Z= 0.123 Angle : 0.585 8.963 3288 Z= 0.293 Chirality : 0.040 0.135 378 Planarity : 0.005 0.050 398 Dihedral : 9.038 140.688 317 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 8.10 % Allowed : 33.20 % 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: 0.72 (0.51), residues: 289 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.62 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 93 HIS 0.002 0.000 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.006 0.001 TYR A 284 ARG 0.001 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 165) hydrogen bonds : angle 3.97815 ( 483) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.14451 ( 4) covalent geometry : bond 0.00282 ( 2413) covalent geometry : angle 0.58492 ( 3284) *********************** 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 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3915 (OUTLIER) cc_final: 0.3689 (m-10) REVERT: A 63 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8153 (ttm-80) REVERT: A 290 ASP cc_start: 0.8663 (m-30) cc_final: 0.8323 (m-30) outliers start: 20 outliers final: 17 residues processed: 79 average time/residue: 0.1150 time to fit residues: 11.0521 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 : 0.271 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.153319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135917 restraints weight = 3874.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139072 restraints weight = 2338.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141125 restraints weight = 1623.197| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2415 Z= 0.144 Angle : 0.611 8.598 3288 Z= 0.310 Chirality : 0.041 0.161 378 Planarity : 0.005 0.050 398 Dihedral : 9.083 141.410 317 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: 0.73 (0.52), residues: 289 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.57 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 165) hydrogen bonds : angle 4.00352 ( 483) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.18518 ( 4) covalent geometry : bond 0.00340 ( 2413) covalent geometry : angle 0.61180 ( 3284) *********************** 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 90 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3863 (OUTLIER) cc_final: 0.3637 (m-10) REVERT: A 63 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8183 (ttm-80) REVERT: A 290 ASP cc_start: 0.8683 (m-30) cc_final: 0.8300 (m-30) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.0985 time to fit residues: 9.7023 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 : 0.242 ------------------------------------------------------------------------------- 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 281 SER Chi-restraints excluded: chain A residue 285 MET 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: 0.0170 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.151669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133885 restraints weight = 4011.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137017 restraints weight = 2408.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139073 restraints weight = 1675.528| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2415 Z= 0.158 Angle : 0.615 7.211 3288 Z= 0.315 Chirality : 0.041 0.158 378 Planarity : 0.005 0.049 398 Dihedral : 9.178 142.911 317 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.69 % Allowed : 32.39 % 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: 0.63 (0.51), residues: 289 helix: 1.59 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.93 (0.65), residues: 80 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 126 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 165) hydrogen bonds : angle 4.04765 ( 483) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.26215 ( 4) covalent geometry : bond 0.00375 ( 2413) covalent geometry : angle 0.61489 ( 3284) *********************** 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 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3881 (OUTLIER) cc_final: 0.3656 (m-10) REVERT: A 63 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8187 (ttm-80) REVERT: A 290 ASP cc_start: 0.8667 (m-30) cc_final: 0.8258 (m-30) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 0.1096 time to fit residues: 10.9487 Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.152087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134263 restraints weight = 4026.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137451 restraints weight = 2380.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139224 restraints weight = 1646.307| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2415 Z= 0.147 Angle : 0.621 9.160 3288 Z= 0.316 Chirality : 0.042 0.161 378 Planarity : 0.005 0.050 398 Dihedral : 9.142 141.896 317 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.50 % Allowed : 32.79 % 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: 0.59 (0.51), residues: 289 helix: 1.41 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.71 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 91 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 165) hydrogen bonds : angle 4.02028 ( 483) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.28880 ( 4) covalent geometry : bond 0.00346 ( 2413) covalent geometry : angle 0.62168 ( 3284) *********************** 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 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3873 (OUTLIER) cc_final: 0.3661 (m-10) REVERT: A 63 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8159 (ttm110) REVERT: A 290 ASP cc_start: 0.8673 (m-30) cc_final: 0.8228 (m-30) outliers start: 21 outliers final: 17 residues processed: 79 average time/residue: 0.1024 time to fit residues: 10.1088 Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 149 CYS 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: 1.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.152406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134880 restraints weight = 3898.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137874 restraints weight = 2337.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140098 restraints weight = 1631.688| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2415 Z= 0.141 Angle : 0.607 8.674 3288 Z= 0.310 Chirality : 0.041 0.163 378 Planarity : 0.005 0.049 398 Dihedral : 9.090 141.135 317 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.69 % Allowed : 32.79 % 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: 0.60 (0.51), residues: 289 helix: 1.42 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.70 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.000 HIS A 189 PHE 0.011 0.001 PHE A 54 TYR 0.007 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 165) hydrogen bonds : angle 4.02323 ( 483) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.28521 ( 4) covalent geometry : bond 0.00329 ( 2413) covalent geometry : angle 0.60752 ( 3284) *********************** 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 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3872 (OUTLIER) cc_final: 0.3670 (m-10) REVERT: A 63 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.8137 (ttm110) REVERT: A 290 ASP cc_start: 0.8643 (m-30) cc_final: 0.8199 (m-30) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.1048 time to fit residues: 10.0522 Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 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 149 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134447 restraints weight = 3915.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137655 restraints weight = 2324.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139869 restraints weight = 1593.919| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2415 Z= 0.149 Angle : 0.616 8.633 3288 Z= 0.314 Chirality : 0.042 0.169 378 Planarity : 0.005 0.050 398 Dihedral : 9.108 141.396 317 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.29 % Allowed : 32.79 % 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: 0.53 (0.51), residues: 289 helix: 1.57 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.000 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 165) hydrogen bonds : angle 4.02518 ( 483) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.32597 ( 4) covalent geometry : bond 0.00348 ( 2413) covalent geometry : angle 0.61597 ( 3284) ********************** 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 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3847 (OUTLIER) cc_final: 0.3638 (m-10) REVERT: A 63 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7981 (ttm110) REVERT: A 190 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9090 (mm-30) REVERT: A 290 ASP cc_start: 0.8654 (m-30) cc_final: 0.8176 (m-30) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.1037 time to fit residues: 10.0193 Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 149 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.151444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133866 restraints weight = 3957.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136934 restraints weight = 2354.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139167 restraints weight = 1628.430| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2415 Z= 0.157 Angle : 0.624 8.495 3288 Z= 0.318 Chirality : 0.042 0.167 378 Planarity : 0.005 0.049 398 Dihedral : 9.133 141.585 317 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 7.69 % Allowed : 32.79 % 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: 0.48 (0.51), residues: 289 helix: 1.54 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.09 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.001 0.000 HIS A 161 PHE 0.011 0.001 PHE A 54 TYR 0.009 0.001 TYR A 126 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 165) hydrogen bonds : angle 4.06248 ( 483) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.36459 ( 4) covalent geometry : bond 0.00371 ( 2413) covalent geometry : angle 0.62438 ( 3284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1103.60 seconds wall clock time: 19 minutes 44.89 seconds (1184.89 seconds total)