Starting phenix.real_space_refine on Sat Apr 26 15:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3o_39749/04_2025/8z3o_39749_neut.cif" } resolution = 3.3 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1430 2.51 5 N 361 2.21 5 O 356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2159 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2159 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 8, 'TRANS': 277} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 2.44, per 1000 atoms: 1.13 Number of scatterers: 2159 At special positions: 0 Unit cell: (48.1, 61.42, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 356 8.00 N 361 7.00 C 1430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 13 " - pdb=" SG CYS R 258 " distance=2.23 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: 0.58 Conformation dependent library (CDL) restraints added in 288.0 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 550 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 80.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 18 through 22 Processing helix chain 'R' and resid 23 through 52 Proline residue: R 37 - end of helix removed outlier: 3.712A pdb=" N ALA R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 83 removed outlier: 4.228A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 93 through 103 removed outlier: 4.399A pdb=" N ILE R 99 " --> pdb=" O GLN R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 124 removed outlier: 4.347A pdb=" N SER R 108 " --> pdb=" O ASN R 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'R' and resid 179 through 195 removed outlier: 3.658A pdb=" N ARG R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE R 185 " --> pdb=" O TRP R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 214 removed outlier: 3.888A pdb=" N GLY R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 255 removed outlier: 3.719A pdb=" N LYS R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP R 224 " --> pdb=" O LYS R 220 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 4.016A pdb=" N TRP R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 264 Processing helix chain 'R' and resid 264 through 275 Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 295 152 hydrogen bonds defined for protein. 450 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: 0.54 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 329 1.32 - 1.44: 688 1.44 - 1.57: 1195 1.57 - 1.69: 0 1.69 - 1.82: 12 Bond restraints: 2224 Sorted by residual: bond pdb=" CA HIS R 17 " pdb=" C HIS R 17 " ideal model delta sigma weight residual 1.528 1.471 0.058 1.07e-02 8.73e+03 2.91e+01 bond pdb=" CA HIS R 17 " pdb=" CB HIS R 17 " ideal model delta sigma weight residual 1.527 1.490 0.038 7.60e-03 1.73e+04 2.46e+01 bond pdb=" CA THR R 14 " pdb=" C THR R 14 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" CA HIS R 175 " pdb=" C HIS R 175 " ideal model delta sigma weight residual 1.520 1.471 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" N ALA R 261 " pdb=" CA ALA R 261 " ideal model delta sigma weight residual 1.459 1.413 0.047 1.19e-02 7.06e+03 1.54e+01 ... (remaining 2219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 2927 2.14 - 4.27: 97 4.27 - 6.41: 19 6.41 - 8.55: 6 8.55 - 10.68: 5 Bond angle restraints: 3054 Sorted by residual: angle pdb=" N GLY R 263 " pdb=" CA GLY R 263 " pdb=" C GLY R 263 " ideal model delta sigma weight residual 112.50 121.93 -9.43 1.16e+00 7.43e-01 6.61e+01 angle pdb=" N HIS R 175 " pdb=" CA HIS R 175 " pdb=" C HIS R 175 " ideal model delta sigma weight residual 108.69 98.01 10.68 1.77e+00 3.19e-01 3.64e+01 angle pdb=" C TYR R 176 " pdb=" N PRO R 177 " pdb=" CA PRO R 177 " ideal model delta sigma weight residual 119.84 112.30 7.54 1.25e+00 6.40e-01 3.63e+01 angle pdb=" N ILE R 178 " pdb=" CA ILE R 178 " pdb=" C ILE R 178 " ideal model delta sigma weight residual 109.30 116.16 -6.86 1.31e+00 5.83e-01 2.74e+01 angle pdb=" N ASP R 85 " pdb=" CA ASP R 85 " pdb=" C ASP R 85 " ideal model delta sigma weight residual 111.90 118.56 -6.66 1.32e+00 5.74e-01 2.55e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 1116 15.05 - 30.09: 97 30.09 - 45.14: 28 45.14 - 60.19: 9 60.19 - 75.23: 4 Dihedral angle restraints: 1254 sinusoidal: 403 harmonic: 851 Sorted by residual: dihedral pdb=" CB CYS R 13 " pdb=" SG CYS R 13 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -142.56 56.56 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CA HIS R 89 " pdb=" C HIS R 89 " pdb=" N GLY R 90 " pdb=" CA GLY R 90 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C ILE R 178 " pdb=" N ILE R 178 " pdb=" CA ILE R 178 " pdb=" CB ILE R 178 " ideal model delta harmonic sigma weight residual -122.00 -133.41 11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 1251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 309 0.085 - 0.171: 47 0.171 - 0.256: 2 0.256 - 0.341: 0 0.341 - 0.427: 1 Chirality restraints: 359 Sorted by residual: chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ASN R 266 " pdb=" N ASN R 266 " pdb=" C ASN R 266 " pdb=" CB ASN R 266 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR R 14 " pdb=" N THR R 14 " pdb=" C THR R 14 " pdb=" CB THR R 14 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 356 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU R 174 " 0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C GLU R 174 " -0.092 2.00e-02 2.50e+03 pdb=" O GLU R 174 " 0.035 2.00e-02 2.50e+03 pdb=" N HIS R 175 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 262 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LYS R 262 " -0.057 2.00e-02 2.50e+03 pdb=" O LYS R 262 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY R 263 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 17 " -0.028 2.00e-02 2.50e+03 2.35e-02 8.29e+00 pdb=" CG HIS R 17 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS R 17 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 17 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS R 17 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS R 17 " -0.023 2.00e-02 2.50e+03 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 841 2.89 - 3.39: 2229 3.39 - 3.89: 3390 3.89 - 4.40: 3520 4.40 - 4.90: 6083 Nonbonded interactions: 16063 Sorted by model distance: nonbonded pdb=" N ASP R 85 " pdb=" OD1 ASP R 85 " model vdw 2.386 3.120 nonbonded pdb=" OH TYR R 102 " pdb=" OE2 GLU R 174 " model vdw 2.420 3.040 nonbonded pdb=" O TYR R 176 " pdb=" N ILE R 178 " model vdw 2.438 3.120 nonbonded pdb=" OD1 ASP R 16 " pdb=" N HIS R 17 " model vdw 2.459 3.120 nonbonded pdb=" OE1 GLN R 79 " pdb=" NE2 HIS R 89 " model vdw 2.460 3.120 ... (remaining 16058 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.030 Process input model: 11.500 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: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.197 2225 Z= 0.483 Angle : 0.985 10.682 3056 Z= 0.579 Chirality : 0.059 0.427 359 Planarity : 0.005 0.053 380 Dihedral : 14.142 75.233 701 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.98 % Allowed : 0.98 % Favored : 98.05 % Cbeta Deviations : 0.36 % 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: 284 helix: 0.65 (0.37), residues: 214 sheet: None (None), residues: 0 loop : -4.02 (0.57), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 87 HIS 0.016 0.002 HIS R 17 PHE 0.022 0.002 PHE R 173 TYR 0.016 0.002 TYR R 80 ARG 0.012 0.001 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.13208 ( 152) hydrogen bonds : angle 6.56585 ( 450) SS BOND : bond 0.19744 ( 1) SS BOND : angle 2.75052 ( 2) covalent geometry : bond 0.00691 ( 2224) covalent geometry : angle 0.98256 ( 3054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.258 Fit side-chains REVERT: R 204 SER cc_start: 0.8232 (p) cc_final: 0.8028 (p) REVERT: R 274 LEU cc_start: 0.8026 (tp) cc_final: 0.7821 (tt) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1191 time to fit residues: 6.7769 Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 GLN R 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111010 restraints weight = 2875.176| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.82 r_work: 0.3261 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2225 Z= 0.160 Angle : 0.655 6.499 3056 Z= 0.337 Chirality : 0.044 0.135 359 Planarity : 0.004 0.034 380 Dihedral : 5.268 27.613 312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.49 % Allowed : 6.83 % Favored : 92.68 % 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: -0.11 (0.51), residues: 284 helix: 0.99 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.65 (0.57), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 146 HIS 0.005 0.001 HIS R 20 PHE 0.015 0.001 PHE R 265 TYR 0.012 0.001 TYR R 80 ARG 0.006 0.001 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 152) hydrogen bonds : angle 4.54308 ( 450) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.55891 ( 2) covalent geometry : bond 0.00367 ( 2224) covalent geometry : angle 0.65551 ( 3054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.232 Fit side-chains REVERT: R 204 SER cc_start: 0.8165 (p) cc_final: 0.7936 (p) REVERT: R 275 THR cc_start: 0.8006 (t) cc_final: 0.7732 (t) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0859 time to fit residues: 4.5415 Evaluate side-chains 35 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.0270 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.0470 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 overall best weight: 0.1514 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.130120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115111 restraints weight = 2806.268| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.90 r_work: 0.3322 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2225 Z= 0.107 Angle : 0.551 5.735 3056 Z= 0.285 Chirality : 0.041 0.176 359 Planarity : 0.003 0.033 380 Dihedral : 4.613 18.309 312 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.49 % Allowed : 9.27 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.52), residues: 284 helix: 1.27 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.57 (0.56), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 254 HIS 0.005 0.001 HIS R 17 PHE 0.022 0.001 PHE R 190 TYR 0.008 0.001 TYR R 106 ARG 0.004 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 152) hydrogen bonds : angle 4.05650 ( 450) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.39902 ( 2) covalent geometry : bond 0.00227 ( 2224) covalent geometry : angle 0.55121 ( 3054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.273 Fit side-chains REVERT: R 248 LEU cc_start: 0.7437 (tt) cc_final: 0.7207 (tp) REVERT: R 275 THR cc_start: 0.7755 (t) cc_final: 0.7549 (t) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0942 time to fit residues: 4.7236 Evaluate side-chains 36 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 2 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 7 optimal weight: 0.0020 chunk 10 optimal weight: 0.1980 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 overall best weight: 0.0622 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119164 restraints weight = 2843.204| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.85 r_work: 0.3385 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2225 Z= 0.098 Angle : 0.511 5.729 3056 Z= 0.265 Chirality : 0.038 0.141 359 Planarity : 0.003 0.029 380 Dihedral : 4.209 16.421 310 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.52), residues: 284 helix: 1.49 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.54 (0.58), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 254 HIS 0.002 0.001 HIS R 17 PHE 0.015 0.001 PHE R 190 TYR 0.008 0.001 TYR R 106 ARG 0.003 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 152) hydrogen bonds : angle 3.84466 ( 450) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.31711 ( 2) covalent geometry : bond 0.00203 ( 2224) covalent geometry : angle 0.51157 ( 3054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1011 time to fit residues: 4.8989 Evaluate side-chains 36 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 GLN R 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114953 restraints weight = 2841.520| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.85 r_work: 0.3303 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2225 Z= 0.114 Angle : 0.520 5.800 3056 Z= 0.270 Chirality : 0.039 0.128 359 Planarity : 0.003 0.028 380 Dihedral : 4.213 17.351 310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.49 % Allowed : 14.15 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.53), residues: 284 helix: 1.50 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.44 (0.59), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 PHE 0.012 0.001 PHE R 190 TYR 0.008 0.001 TYR R 80 ARG 0.003 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 152) hydrogen bonds : angle 3.86772 ( 450) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.13360 ( 2) covalent geometry : bond 0.00254 ( 2224) covalent geometry : angle 0.51998 ( 3054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.215 Fit side-chains REVERT: R 100 LEU cc_start: 0.8583 (mt) cc_final: 0.8375 (mp) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0919 time to fit residues: 4.7880 Evaluate side-chains 40 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.2980 chunk 7 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 overall best weight: 0.1788 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.131214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115674 restraints weight = 2848.583| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.88 r_work: 0.3334 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 2225 Z= 0.107 Angle : 0.520 5.782 3056 Z= 0.268 Chirality : 0.039 0.130 359 Planarity : 0.003 0.027 380 Dihedral : 4.170 16.815 310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.98 % Allowed : 14.15 % Favored : 84.88 % 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: 284 helix: 1.54 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.34 (0.60), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 254 HIS 0.002 0.001 HIS R 17 PHE 0.022 0.001 PHE R 190 TYR 0.007 0.001 TYR R 106 ARG 0.002 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 152) hydrogen bonds : angle 3.87492 ( 450) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.15677 ( 2) covalent geometry : bond 0.00242 ( 2224) covalent geometry : angle 0.52056 ( 3054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.232 Fit side-chains REVERT: R 100 LEU cc_start: 0.8602 (mt) cc_final: 0.8380 (mp) REVERT: R 249 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7706 (mt) REVERT: R 275 THR cc_start: 0.7536 (t) cc_final: 0.7226 (t) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.0895 time to fit residues: 4.3819 Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.0030 overall best weight: 0.2488 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115503 restraints weight = 2904.213| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.84 r_work: 0.3319 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2225 Z= 0.115 Angle : 0.522 5.796 3056 Z= 0.269 Chirality : 0.039 0.118 359 Planarity : 0.003 0.028 380 Dihedral : 4.161 17.076 310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.98 % Allowed : 14.15 % Favored : 84.88 % 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: 0.79 (0.52), residues: 284 helix: 1.54 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.15 (0.62), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 254 HIS 0.002 0.001 HIS R 17 PHE 0.021 0.001 PHE R 190 TYR 0.007 0.001 TYR R 106 ARG 0.002 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 152) hydrogen bonds : angle 3.90172 ( 450) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.11297 ( 2) covalent geometry : bond 0.00259 ( 2224) covalent geometry : angle 0.52238 ( 3054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.235 Fit side-chains REVERT: R 100 LEU cc_start: 0.8599 (mt) cc_final: 0.8373 (mp) REVERT: R 161 GLU cc_start: 0.7490 (pt0) cc_final: 0.7198 (pt0) REVERT: R 249 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7768 (mt) REVERT: R 275 THR cc_start: 0.7632 (t) cc_final: 0.7405 (t) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.0939 time to fit residues: 4.4685 Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 0.0980 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 overall best weight: 0.1276 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118222 restraints weight = 2928.523| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.87 r_work: 0.3353 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 2225 Z= 0.101 Angle : 0.504 5.764 3056 Z= 0.259 Chirality : 0.038 0.122 359 Planarity : 0.003 0.028 380 Dihedral : 4.008 15.884 310 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.49 % Allowed : 14.15 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.52), residues: 284 helix: 1.64 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.12 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 254 HIS 0.002 0.000 HIS R 17 PHE 0.022 0.001 PHE R 190 TYR 0.007 0.001 TYR R 106 ARG 0.002 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 152) hydrogen bonds : angle 3.81820 ( 450) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.21480 ( 2) covalent geometry : bond 0.00219 ( 2224) covalent geometry : angle 0.50462 ( 3054) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.237 Fit side-chains REVERT: R 100 LEU cc_start: 0.8601 (mt) cc_final: 0.8368 (mp) REVERT: R 161 GLU cc_start: 0.7432 (pt0) cc_final: 0.7116 (pt0) REVERT: R 249 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7754 (mt) REVERT: R 275 THR cc_start: 0.7453 (t) cc_final: 0.7184 (t) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1035 time to fit residues: 4.9641 Evaluate side-chains 36 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.125753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110956 restraints weight = 2879.617| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.83 r_work: 0.3248 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2225 Z= 0.184 Angle : 0.597 6.019 3056 Z= 0.308 Chirality : 0.042 0.130 359 Planarity : 0.003 0.029 380 Dihedral : 4.472 19.046 310 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.49 % Allowed : 15.12 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.52), residues: 284 helix: 1.42 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.13 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 146 HIS 0.003 0.001 HIS R 17 PHE 0.017 0.001 PHE R 111 TYR 0.015 0.001 TYR R 80 ARG 0.002 0.001 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 152) hydrogen bonds : angle 4.13786 ( 450) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.18912 ( 2) covalent geometry : bond 0.00428 ( 2224) covalent geometry : angle 0.59727 ( 3054) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.235 Fit side-chains REVERT: R 100 LEU cc_start: 0.8621 (mt) cc_final: 0.8399 (mp) REVERT: R 102 TYR cc_start: 0.7769 (m-80) cc_final: 0.7555 (m-80) REVERT: R 275 THR cc_start: 0.7810 (t) cc_final: 0.7566 (t) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.0848 time to fit residues: 4.9573 Evaluate side-chains 43 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 6 optimal weight: 0.0070 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.128946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113932 restraints weight = 2859.922| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.92 r_work: 0.3294 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2225 Z= 0.121 Angle : 0.552 5.802 3056 Z= 0.283 Chirality : 0.039 0.122 359 Planarity : 0.003 0.030 380 Dihedral : 4.359 17.609 310 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.52), residues: 284 helix: 1.47 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.07 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 PHE 0.021 0.001 PHE R 190 TYR 0.007 0.001 TYR R 106 ARG 0.002 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 152) hydrogen bonds : angle 4.01774 ( 450) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.09352 ( 2) covalent geometry : bond 0.00273 ( 2224) covalent geometry : angle 0.55224 ( 3054) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.229 Fit side-chains REVERT: R 100 LEU cc_start: 0.8613 (mt) cc_final: 0.8376 (mp) REVERT: R 102 TYR cc_start: 0.7677 (m-80) cc_final: 0.7471 (m-80) REVERT: R 275 THR cc_start: 0.7649 (t) cc_final: 0.7421 (t) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0888 time to fit residues: 4.3372 Evaluate side-chains 36 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0000 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3442 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.128032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113476 restraints weight = 2900.284| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.84 r_work: 0.3288 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2225 Z= 0.133 Angle : 0.569 5.821 3056 Z= 0.290 Chirality : 0.039 0.118 359 Planarity : 0.003 0.030 380 Dihedral : 4.318 17.635 310 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % 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 (0.52), residues: 284 helix: 1.43 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.25 (0.61), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 PHE 0.019 0.001 PHE R 190 TYR 0.009 0.001 TYR R 80 ARG 0.002 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 152) hydrogen bonds : angle 4.03699 ( 450) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.05491 ( 2) covalent geometry : bond 0.00309 ( 2224) covalent geometry : angle 0.56924 ( 3054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.98 seconds wall clock time: 29 minutes 21.77 seconds (1761.77 seconds total)