Starting phenix.real_space_refine on Fri Aug 22 12:40:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794.map" model { file = "/net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z67_39794/08_2025/8z67_39794_neut.cif" } resolution = 3.2 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= 0.022 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 14 5.16 5 C 1527 2.51 5 N 380 2.21 5 O 383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2304 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2304 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 284} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 9, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 0.91, per 1000 atoms: 0.39 Number of scatterers: 2304 At special positions: 0 Unit cell: (74.692, 58.912, 62.068, 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 14 16.00 O 383 8.00 N 380 7.00 C 1527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 96.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 81.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'R' and resid 18 through 48 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 3.593A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 3.695A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.528A pdb=" N HIS R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 259 through 264 Processing helix chain 'R' and resid 264 through 275 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 Processing sheet with id=AA1, first strand: chain 'R' and resid 158 through 160 removed outlier: 3.769A pdb=" N PHE R 159 " --> pdb=" O PHE R 167 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 522 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: 0.38 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 342 1.29 - 1.42: 718 1.42 - 1.55: 1295 1.55 - 1.68: 3 1.68 - 1.82: 18 Bond restraints: 2376 Sorted by residual: bond pdb=" CA ASP R 12 " pdb=" C ASP R 12 " ideal model delta sigma weight residual 1.531 1.389 0.142 1.15e-02 7.56e+03 1.53e+02 bond pdb=" CA ASN R 82 " pdb=" C ASN R 82 " ideal model delta sigma weight residual 1.522 1.426 0.096 1.18e-02 7.18e+03 6.67e+01 bond pdb=" C HIS R 17 " pdb=" O HIS R 17 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.33e-02 5.65e+03 3.97e+01 bond pdb=" N SER R 13 " pdb=" CA SER R 13 " ideal model delta sigma weight residual 1.462 1.378 0.084 1.35e-02 5.49e+03 3.86e+01 bond pdb=" N ASN R 82 " pdb=" CA ASN R 82 " ideal model delta sigma weight residual 1.460 1.388 0.072 1.17e-02 7.31e+03 3.77e+01 ... (remaining 2371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 3204 3.94 - 7.89: 41 7.89 - 11.83: 5 11.83 - 15.78: 1 15.78 - 19.72: 1 Bond angle restraints: 3252 Sorted by residual: angle pdb=" N ILE R 84 " pdb=" CA ILE R 84 " pdb=" C ILE R 84 " ideal model delta sigma weight residual 111.77 125.02 -13.25 1.04e+00 9.25e-01 1.62e+02 angle pdb=" N GLY R 88 " pdb=" CA GLY R 88 " pdb=" C GLY R 88 " ideal model delta sigma weight residual 112.77 123.90 -11.13 1.28e+00 6.10e-01 7.56e+01 angle pdb=" N HIS R 85 " pdb=" CA HIS R 85 " pdb=" C HIS R 85 " ideal model delta sigma weight residual 111.24 100.16 11.08 1.29e+00 6.01e-01 7.38e+01 angle pdb=" N GLY R 259 " pdb=" CA GLY R 259 " pdb=" C GLY R 259 " ideal model delta sigma weight residual 113.18 93.46 19.72 2.37e+00 1.78e-01 6.92e+01 angle pdb=" C PRO R 87 " pdb=" N GLY R 88 " pdb=" CA GLY R 88 " ideal model delta sigma weight residual 120.00 127.97 -7.97 1.10e+00 8.26e-01 5.25e+01 ... (remaining 3247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 1189 14.57 - 29.14: 121 29.14 - 43.71: 37 43.71 - 58.28: 3 58.28 - 72.85: 4 Dihedral angle restraints: 1354 sinusoidal: 479 harmonic: 875 Sorted by residual: dihedral pdb=" N ILE R 84 " pdb=" C ILE R 84 " pdb=" CA ILE R 84 " pdb=" CB ILE R 84 " ideal model delta harmonic sigma weight residual 123.40 137.69 -14.29 0 2.50e+00 1.60e-01 3.27e+01 dihedral pdb=" C ILE R 84 " pdb=" N ILE R 84 " pdb=" CA ILE R 84 " pdb=" CB ILE R 84 " ideal model delta harmonic sigma weight residual -122.00 -135.56 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C HIS R 17 " pdb=" N HIS R 17 " pdb=" CA HIS R 17 " pdb=" CB HIS R 17 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 1351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 347 0.120 - 0.239: 19 0.239 - 0.359: 4 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA ILE R 84 " pdb=" N ILE R 84 " pdb=" C ILE R 84 " pdb=" CB ILE R 84 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CB VAL R 297 " pdb=" CA VAL R 297 " pdb=" CG1 VAL R 297 " pdb=" CG2 VAL R 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA HIS R 17 " pdb=" N HIS R 17 " pdb=" C HIS R 17 " pdb=" CB HIS R 17 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 369 not shown) Planarity restraints: 401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 253 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C GLY R 253 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY R 253 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG R 254 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 79 " 0.033 2.00e-02 2.50e+03 2.44e-02 8.92e+00 pdb=" CG HIS R 79 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS R 79 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS R 79 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS R 79 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS R 79 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 10 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C HIS R 10 " 0.043 2.00e-02 2.50e+03 pdb=" O HIS R 10 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL R 11 " -0.014 2.00e-02 2.50e+03 ... (remaining 398 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 4 2.35 - 2.98: 1164 2.98 - 3.62: 3779 3.62 - 4.26: 5255 4.26 - 4.90: 9168 Nonbonded interactions: 19370 Sorted by model distance: nonbonded pdb=" CB SER R 13 " pdb=" OD1 ASP R 16 " model vdw 1.708 3.440 nonbonded pdb=" CB SER R 13 " pdb=" CG ASP R 16 " model vdw 2.037 3.670 nonbonded pdb=" N GLY R 259 " pdb=" N PHE R 260 " model vdw 2.166 2.560 nonbonded pdb=" O LEU R 272 " pdb=" OG1 THR R 275 " model vdw 2.325 3.040 nonbonded pdb=" CB SER R 13 " pdb=" OD2 ASP R 16 " model vdw 2.355 3.440 ... (remaining 19365 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 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 : 0.011 0.142 2377 Z= 0.762 Angle : 1.101 19.722 3254 Z= 0.672 Chirality : 0.075 0.599 372 Planarity : 0.006 0.037 401 Dihedral : 13.562 72.849 787 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.71 % Allowed : 4.27 % Favored : 94.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 8.33 % 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: 0.94 (0.50), residues: 295 helix: 1.47 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -2.86 (0.71), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 247 TYR 0.015 0.002 TYR R 102 PHE 0.033 0.002 PHE R 169 TRP 0.021 0.002 TRP R 256 HIS 0.025 0.003 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.01088 ( 2376) covalent geometry : angle 1.09868 ( 3252) SS BOND : bond 0.00204 ( 1) SS BOND : angle 2.92451 ( 2) hydrogen bonds : bond 0.10979 ( 176) hydrogen bonds : angle 5.46506 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.095 Fit side-chains REVERT: R 181 MET cc_start: 0.6336 (tpt) cc_final: 0.5852 (tpt) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.1180 time to fit residues: 3.9658 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110283 restraints weight = 2910.002| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.23 r_work: 0.3256 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2377 Z= 0.181 Angle : 0.575 6.673 3254 Z= 0.302 Chirality : 0.043 0.151 372 Planarity : 0.004 0.035 401 Dihedral : 4.349 17.208 326 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.14 % Allowed : 8.55 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.23 (0.49), residues: 295 helix: 1.58 (0.33), residues: 240 sheet: None (None), residues: 0 loop : -2.67 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 185 TYR 0.015 0.002 TYR R 102 PHE 0.023 0.002 PHE R 169 TRP 0.017 0.002 TRP R 256 HIS 0.006 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 2376) covalent geometry : angle 0.57375 ( 3252) SS BOND : bond 0.00254 ( 1) SS BOND : angle 1.52428 ( 2) hydrogen bonds : bond 0.04137 ( 176) hydrogen bonds : angle 4.51956 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.084 Fit side-chains REVERT: R 181 MET cc_start: 0.7518 (tpt) cc_final: 0.7037 (tpt) REVERT: R 269 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7576 (m-70) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 0.1264 time to fit residues: 4.2156 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109387 restraints weight = 2955.152| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.41 r_work: 0.3168 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2377 Z= 0.141 Angle : 0.534 6.663 3254 Z= 0.280 Chirality : 0.041 0.207 372 Planarity : 0.004 0.033 401 Dihedral : 3.894 14.438 322 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 11.54 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.65 (0.50), residues: 295 helix: 2.06 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.70 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.014 0.001 TYR R 102 PHE 0.014 0.002 PHE R 169 TRP 0.010 0.001 TRP R 256 HIS 0.004 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2376) covalent geometry : angle 0.53297 ( 3252) SS BOND : bond 0.00247 ( 1) SS BOND : angle 1.29741 ( 2) hydrogen bonds : bond 0.03864 ( 176) hydrogen bonds : angle 4.36055 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.087 Fit side-chains REVERT: R 39 LEU cc_start: 0.7639 (tp) cc_final: 0.7398 (tt) REVERT: R 181 MET cc_start: 0.7509 (tpt) cc_final: 0.7072 (tpt) REVERT: R 269 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7487 (m-70) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.1264 time to fit residues: 4.2207 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107854 restraints weight = 2909.531| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.41 r_work: 0.3257 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2377 Z= 0.175 Angle : 0.556 6.605 3254 Z= 0.293 Chirality : 0.044 0.217 372 Planarity : 0.004 0.033 401 Dihedral : 4.001 19.465 322 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.28 % Allowed : 12.39 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.42 (0.50), residues: 295 helix: 1.77 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.75 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 115 TYR 0.013 0.002 TYR R 102 PHE 0.014 0.002 PHE R 169 TRP 0.010 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 2376) covalent geometry : angle 0.55581 ( 3252) SS BOND : bond 0.00282 ( 1) SS BOND : angle 1.23299 ( 2) hydrogen bonds : bond 0.03998 ( 176) hydrogen bonds : angle 4.34248 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.102 Fit side-chains REVERT: R 39 LEU cc_start: 0.7664 (tp) cc_final: 0.7431 (tt) REVERT: R 181 MET cc_start: 0.7491 (tpt) cc_final: 0.7053 (tpt) REVERT: R 247 ARG cc_start: 0.6555 (mtm110) cc_final: 0.6220 (mtp-110) REVERT: R 269 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7681 (m-70) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.1397 time to fit residues: 4.0356 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107067 restraints weight = 2968.043| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.53 r_work: 0.3260 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2377 Z= 0.129 Angle : 0.515 6.625 3254 Z= 0.271 Chirality : 0.042 0.251 372 Planarity : 0.003 0.032 401 Dihedral : 3.851 19.739 322 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.71 % Allowed : 12.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.74 (0.50), residues: 295 helix: 1.99 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.55 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 185 TYR 0.013 0.001 TYR R 102 PHE 0.011 0.001 PHE R 169 TRP 0.007 0.001 TRP R 256 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2376) covalent geometry : angle 0.51396 ( 3252) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.12806 ( 2) hydrogen bonds : bond 0.03712 ( 176) hydrogen bonds : angle 4.20144 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.082 Fit side-chains REVERT: R 39 LEU cc_start: 0.7574 (tp) cc_final: 0.7339 (tt) REVERT: R 181 MET cc_start: 0.7428 (tpt) cc_final: 0.7035 (tpt) REVERT: R 247 ARG cc_start: 0.6466 (mtm110) cc_final: 0.6098 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.1223 time to fit residues: 4.0948 Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111229 restraints weight = 2905.693| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.39 r_work: 0.3279 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2377 Z= 0.159 Angle : 0.536 6.574 3254 Z= 0.281 Chirality : 0.043 0.257 372 Planarity : 0.004 0.032 401 Dihedral : 3.860 18.727 322 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.85 % Allowed : 12.39 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.55 (0.50), residues: 295 helix: 1.87 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.74 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.013 0.001 TYR R 102 PHE 0.011 0.002 PHE R 97 TRP 0.010 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2376) covalent geometry : angle 0.53513 ( 3252) SS BOND : bond 0.00210 ( 1) SS BOND : angle 1.12761 ( 2) hydrogen bonds : bond 0.03870 ( 176) hydrogen bonds : angle 4.23577 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.082 Fit side-chains REVERT: R 39 LEU cc_start: 0.7704 (tp) cc_final: 0.7470 (tt) REVERT: R 181 MET cc_start: 0.7490 (tpt) cc_final: 0.7102 (tpt) REVERT: R 247 ARG cc_start: 0.6585 (mtm110) cc_final: 0.6222 (mtp-110) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1195 time to fit residues: 4.0041 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111352 restraints weight = 2876.160| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.38 r_work: 0.3282 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2377 Z= 0.153 Angle : 0.528 6.576 3254 Z= 0.277 Chirality : 0.043 0.265 372 Planarity : 0.004 0.032 401 Dihedral : 3.813 17.768 322 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.28 % Allowed : 13.68 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.60 (0.50), residues: 295 helix: 1.90 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.71 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.012 0.001 TYR R 76 PHE 0.011 0.002 PHE R 97 TRP 0.009 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2376) covalent geometry : angle 0.52708 ( 3252) SS BOND : bond 0.00262 ( 1) SS BOND : angle 1.10812 ( 2) hydrogen bonds : bond 0.03860 ( 176) hydrogen bonds : angle 4.21702 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.085 Fit side-chains REVERT: R 39 LEU cc_start: 0.7676 (tp) cc_final: 0.7450 (tt) REVERT: R 181 MET cc_start: 0.7433 (tpt) cc_final: 0.7077 (tpt) REVERT: R 247 ARG cc_start: 0.6583 (mtm110) cc_final: 0.6215 (mtp-110) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.1321 time to fit residues: 4.1170 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109049 restraints weight = 2868.774| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.44 r_work: 0.3249 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2377 Z= 0.143 Angle : 0.524 6.584 3254 Z= 0.276 Chirality : 0.043 0.279 372 Planarity : 0.004 0.032 401 Dihedral : 3.771 16.082 322 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 13.25 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.69 (0.50), residues: 295 helix: 1.95 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.54 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.013 0.001 TYR R 102 PHE 0.011 0.002 PHE R 93 TRP 0.009 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 2376) covalent geometry : angle 0.52300 ( 3252) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.08121 ( 2) hydrogen bonds : bond 0.03793 ( 176) hydrogen bonds : angle 4.18112 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.090 Fit side-chains REVERT: R 39 LEU cc_start: 0.7590 (tp) cc_final: 0.7374 (tt) REVERT: R 181 MET cc_start: 0.7413 (tpt) cc_final: 0.6977 (tpt) REVERT: R 247 ARG cc_start: 0.6539 (mtm110) cc_final: 0.6177 (mtp-110) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.1138 time to fit residues: 3.3398 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105089 restraints weight = 3045.371| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.61 r_work: 0.3236 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2377 Z= 0.168 Angle : 0.543 6.571 3254 Z= 0.285 Chirality : 0.044 0.287 372 Planarity : 0.004 0.032 401 Dihedral : 3.819 15.748 322 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.55 (0.50), residues: 295 helix: 1.85 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.65 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.013 0.002 TYR R 76 PHE 0.012 0.002 PHE R 97 TRP 0.010 0.001 TRP R 40 HIS 0.006 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2376) covalent geometry : angle 0.54219 ( 3252) SS BOND : bond 0.00279 ( 1) SS BOND : angle 1.05557 ( 2) hydrogen bonds : bond 0.03925 ( 176) hydrogen bonds : angle 4.22668 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.083 Fit side-chains REVERT: R 39 LEU cc_start: 0.7592 (tp) cc_final: 0.7386 (tt) REVERT: R 181 MET cc_start: 0.7437 (tpt) cc_final: 0.6954 (tpt) REVERT: R 247 ARG cc_start: 0.6547 (mtm110) cc_final: 0.6201 (mtp-110) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.1241 time to fit residues: 3.7333 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 10 HIS R 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111203 restraints weight = 2945.909| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.40 r_work: 0.3267 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2377 Z= 0.154 Angle : 0.533 6.578 3254 Z= 0.280 Chirality : 0.044 0.297 372 Planarity : 0.004 0.032 401 Dihedral : 3.786 14.354 322 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.85 % Allowed : 14.53 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.59 (0.50), residues: 295 helix: 1.88 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.66 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.013 0.001 TYR R 102 PHE 0.011 0.002 PHE R 97 TRP 0.010 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 2376) covalent geometry : angle 0.53282 ( 3252) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.02324 ( 2) hydrogen bonds : bond 0.03868 ( 176) hydrogen bonds : angle 4.20319 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.052 Fit side-chains REVERT: R 39 LEU cc_start: 0.7669 (tp) cc_final: 0.7457 (tt) REVERT: R 181 MET cc_start: 0.7434 (tpt) cc_final: 0.6943 (tpt) REVERT: R 247 ARG cc_start: 0.6599 (mtm110) cc_final: 0.6240 (mtp-110) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0938 time to fit residues: 2.7282 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111158 restraints weight = 2916.206| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.40 r_work: 0.3272 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2377 Z= 0.144 Angle : 0.524 6.590 3254 Z= 0.276 Chirality : 0.043 0.298 372 Planarity : 0.004 0.032 401 Dihedral : 3.711 12.198 322 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 14.53 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.70 (0.50), residues: 295 helix: 1.95 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.50 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 115 TYR 0.012 0.001 TYR R 102 PHE 0.010 0.002 PHE R 93 TRP 0.009 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2376) covalent geometry : angle 0.52360 ( 3252) SS BOND : bond 0.00280 ( 1) SS BOND : angle 1.00753 ( 2) hydrogen bonds : bond 0.03814 ( 176) hydrogen bonds : angle 4.17021 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 792.48 seconds wall clock time: 14 minutes 15.29 seconds (855.29 seconds total)