Starting phenix.real_space_refine on Wed Sep 17 03:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3o_39749/09_2025/8z3o_39749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3o_39749/09_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_39749/09_2025/8z3o_39749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3o_39749/09_2025/8z3o_39749.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3o_39749/09_2025/8z3o_39749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3o_39749/09_2025/8z3o_39749_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 0.52, per 1000 atoms: 0.24 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: 0.14 Conformation dependent library (CDL) restraints added in 53.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.04 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: 0.18 Time building geometry restraints manager: 0.17 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.800 Find NCS groups from input model: 0.000 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG R 128 TYR 0.016 0.002 TYR R 80 PHE 0.022 0.002 PHE R 173 TRP 0.006 0.001 TRP R 87 HIS 0.016 0.002 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 2224) covalent geometry : angle 0.98256 ( 3054) SS BOND : bond 0.19744 ( 1) SS BOND : angle 2.75052 ( 2) hydrogen bonds : bond 0.13208 ( 152) hydrogen bonds : angle 6.56585 ( 450) *********************** 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 : 0.083 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: 0.0605 time to fit residues: 3.3497 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 : 0.111 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.125043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110596 restraints weight = 2856.676| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.84 r_work: 0.3209 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2225 Z= 0.170 Angle : 0.662 6.592 3056 Z= 0.340 Chirality : 0.044 0.136 359 Planarity : 0.004 0.034 380 Dihedral : 5.261 27.054 312 Min Nonbonded Distance : 2.476 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.51), residues: 284 helix: 0.97 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.65 (0.57), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 128 TYR 0.012 0.001 TYR R 80 PHE 0.015 0.001 PHE R 265 TRP 0.003 0.001 TRP R 87 HIS 0.004 0.001 HIS R 20 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2224) covalent geometry : angle 0.66170 ( 3054) SS BOND : bond 0.00456 ( 1) SS BOND : angle 0.57715 ( 2) hydrogen bonds : bond 0.05023 ( 152) hydrogen bonds : angle 4.58979 ( 450) *********************** 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 46 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.089 Fit side-chains REVERT: R 204 SER cc_start: 0.8162 (p) cc_final: 0.7940 (p) REVERT: R 275 THR cc_start: 0.8022 (t) cc_final: 0.7762 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0346 time to fit residues: 2.1370 Evaluate side-chains 41 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.126841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112067 restraints weight = 2929.323| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.89 r_work: 0.3274 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2225 Z= 0.124 Angle : 0.577 5.800 3056 Z= 0.298 Chirality : 0.041 0.143 359 Planarity : 0.003 0.035 380 Dihedral : 4.771 19.135 312 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.49 % Allowed : 11.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.52), residues: 284 helix: 1.18 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.57 (0.57), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 128 TYR 0.008 0.001 TYR R 106 PHE 0.019 0.001 PHE R 190 TRP 0.006 0.001 TRP R 254 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2224) covalent geometry : angle 0.57681 ( 3054) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.36379 ( 2) hydrogen bonds : bond 0.04168 ( 152) hydrogen bonds : angle 4.15991 ( 450) *********************** 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 : 0.077 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0397 time to fit residues: 1.9683 Evaluate side-chains 34 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109946 restraints weight = 2879.232| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.86 r_work: 0.3237 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2225 Z= 0.156 Angle : 0.578 5.873 3056 Z= 0.301 Chirality : 0.041 0.134 359 Planarity : 0.003 0.035 380 Dihedral : 4.722 19.283 310 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 10.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.52), residues: 284 helix: 1.25 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.42 (0.60), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 128 TYR 0.010 0.001 TYR R 80 PHE 0.015 0.001 PHE R 111 TRP 0.005 0.001 TRP R 254 HIS 0.004 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2224) covalent geometry : angle 0.57798 ( 3054) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.16043 ( 2) hydrogen bonds : bond 0.04666 ( 152) hydrogen bonds : angle 4.12539 ( 450) *********************** 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 46 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.079 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.0344 time to fit residues: 2.0528 Evaluate side-chains 42 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 20 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.125610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110588 restraints weight = 2925.088| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.97 r_work: 0.3250 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2225 Z= 0.144 Angle : 0.567 6.159 3056 Z= 0.293 Chirality : 0.041 0.148 359 Planarity : 0.003 0.036 380 Dihedral : 4.621 18.721 310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.44 % Allowed : 12.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.52), residues: 284 helix: 1.32 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.36 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 128 TYR 0.008 0.001 TYR R 106 PHE 0.013 0.001 PHE R 111 TRP 0.006 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2224) covalent geometry : angle 0.56750 ( 3054) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.09092 ( 2) hydrogen bonds : bond 0.04368 ( 152) hydrogen bonds : angle 4.07198 ( 450) *********************** 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 45 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.077 Fit side-chains REVERT: R 173 PHE cc_start: 0.8158 (t80) cc_final: 0.7492 (t80) REVERT: R 275 THR cc_start: 0.7787 (t) cc_final: 0.7532 (t) outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 0.0364 time to fit residues: 2.1658 Evaluate side-chains 45 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 236 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.124173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109273 restraints weight = 2834.790| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.90 r_work: 0.3231 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2225 Z= 0.168 Angle : 0.584 5.916 3056 Z= 0.302 Chirality : 0.042 0.151 359 Planarity : 0.003 0.036 380 Dihedral : 4.688 18.960 310 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.95 % Allowed : 13.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.52), residues: 284 helix: 1.24 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.24 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 128 TYR 0.010 0.001 TYR R 102 PHE 0.015 0.001 PHE R 111 TRP 0.005 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 2224) covalent geometry : angle 0.58391 ( 3054) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.06768 ( 2) hydrogen bonds : bond 0.04792 ( 152) hydrogen bonds : angle 4.15162 ( 450) *********************** 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 47 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.079 Fit side-chains REVERT: R 72 CYS cc_start: 0.8159 (t) cc_final: 0.7847 (t) REVERT: R 161 GLU cc_start: 0.7834 (pt0) cc_final: 0.7594 (pt0) REVERT: R 275 THR cc_start: 0.7901 (t) cc_final: 0.7623 (t) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.0331 time to fit residues: 2.0706 Evaluate side-chains 47 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 236 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108263 restraints weight = 2878.184| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.91 r_work: 0.3221 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2225 Z= 0.179 Angle : 0.596 6.440 3056 Z= 0.309 Chirality : 0.042 0.131 359 Planarity : 0.003 0.036 380 Dihedral : 4.776 18.943 310 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.44 % Allowed : 15.61 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.52), residues: 284 helix: 1.21 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.10 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 128 TYR 0.009 0.001 TYR R 80 PHE 0.015 0.001 PHE R 111 TRP 0.006 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2224) covalent geometry : angle 0.59611 ( 3054) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.08651 ( 2) hydrogen bonds : bond 0.04960 ( 152) hydrogen bonds : angle 4.22395 ( 450) *********************** 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 47 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.078 Fit side-chains REVERT: R 72 CYS cc_start: 0.8150 (t) cc_final: 0.7845 (t) REVERT: R 161 GLU cc_start: 0.7863 (pt0) cc_final: 0.7365 (pt0) REVERT: R 275 THR cc_start: 0.8012 (t) cc_final: 0.7745 (t) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.0345 time to fit residues: 2.1011 Evaluate side-chains 43 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 236 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.125259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110632 restraints weight = 2857.630| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.90 r_work: 0.3250 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2225 Z= 0.137 Angle : 0.560 5.835 3056 Z= 0.289 Chirality : 0.041 0.148 359 Planarity : 0.003 0.036 380 Dihedral : 4.583 18.225 310 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.52), residues: 284 helix: 1.32 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.07 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 128 TYR 0.008 0.001 TYR R 102 PHE 0.013 0.001 PHE R 190 TRP 0.005 0.001 TRP R 254 HIS 0.004 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2224) covalent geometry : angle 0.56003 ( 3054) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.04645 ( 2) hydrogen bonds : bond 0.04318 ( 152) hydrogen bonds : angle 4.09973 ( 450) *********************** 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 46 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.073 Fit side-chains REVERT: R 72 CYS cc_start: 0.8138 (t) cc_final: 0.7836 (t) REVERT: R 156 PHE cc_start: 0.7588 (m-80) cc_final: 0.7332 (m-80) REVERT: R 161 GLU cc_start: 0.7706 (pt0) cc_final: 0.7440 (pt0) REVERT: R 275 THR cc_start: 0.7877 (t) cc_final: 0.7613 (t) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.0308 time to fit residues: 1.8613 Evaluate side-chains 44 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110438 restraints weight = 2875.669| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.89 r_work: 0.3246 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2225 Z= 0.140 Angle : 0.570 5.859 3056 Z= 0.292 Chirality : 0.041 0.135 359 Planarity : 0.003 0.036 380 Dihedral : 4.556 17.850 310 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.52), residues: 284 helix: 1.34 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.11 (0.62), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 128 TYR 0.008 0.001 TYR R 106 PHE 0.013 0.001 PHE R 111 TRP 0.005 0.001 TRP R 254 HIS 0.004 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2224) covalent geometry : angle 0.57000 ( 3054) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.03390 ( 2) hydrogen bonds : bond 0.04395 ( 152) hydrogen bonds : angle 4.08970 ( 450) *********************** 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: 3 poor density : 42 time to evaluate : 0.080 Fit side-chains REVERT: R 72 CYS cc_start: 0.8148 (t) cc_final: 0.7842 (t) REVERT: R 156 PHE cc_start: 0.7571 (m-80) cc_final: 0.7281 (m-80) REVERT: R 161 GLU cc_start: 0.7695 (pt0) cc_final: 0.7419 (pt0) REVERT: R 275 THR cc_start: 0.7861 (t) cc_final: 0.7597 (t) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.0311 time to fit residues: 1.8431 Evaluate side-chains 45 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 236 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 23 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.127612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113275 restraints weight = 2908.780| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.85 r_work: 0.3292 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2225 Z= 0.116 Angle : 0.547 5.813 3056 Z= 0.280 Chirality : 0.041 0.138 359 Planarity : 0.003 0.036 380 Dihedral : 4.415 17.102 310 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.52), residues: 284 helix: 1.47 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.11 (0.62), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 128 TYR 0.009 0.001 TYR R 106 PHE 0.014 0.001 PHE R 190 TRP 0.005 0.001 TRP R 254 HIS 0.003 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2224) covalent geometry : angle 0.54762 ( 3054) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.08131 ( 2) hydrogen bonds : bond 0.03884 ( 152) hydrogen bonds : angle 4.00699 ( 450) ********************** 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 39 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.052 Fit side-chains REVERT: R 161 GLU cc_start: 0.7556 (pt0) cc_final: 0.7075 (pt0) REVERT: R 275 THR cc_start: 0.7670 (t) cc_final: 0.7422 (t) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0287 time to fit residues: 1.4914 Evaluate side-chains 38 residues out of total 257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 236 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.0050 chunk 20 optimal weight: 0.0070 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.1218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116296 restraints weight = 2934.701| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.95 r_work: 0.3313 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2750 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= 0.103 Angle : 0.538 6.459 3056 Z= 0.271 Chirality : 0.040 0.159 359 Planarity : 0.003 0.036 380 Dihedral : 4.154 16.023 310 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.98 % Allowed : 16.10 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.53), residues: 284 helix: 1.61 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.26 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 128 TYR 0.009 0.001 TYR R 106 PHE 0.015 0.001 PHE R 190 TRP 0.005 0.001 TRP R 146 HIS 0.003 0.000 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 2224) covalent geometry : angle 0.53828 ( 3054) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.15470 ( 2) hydrogen bonds : bond 0.03328 ( 152) hydrogen bonds : angle 3.86952 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 802.81 seconds wall clock time: 14 minutes 28.74 seconds (868.74 seconds total)