Starting phenix.real_space_refine on Wed Jul 1 20:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191.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 { model { file = "/net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kex_37191/07_2026/8kex_37191.map" } 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 16 5.16 5 C 1328 2.51 5 N 314 2.21 5 O 329 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1988 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1956 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'JW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.02, per 1000 atoms: 0.51 Number of scatterers: 1988 At special positions: 0 Unit cell: (80.08, 56.16, 67.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 1 15.00 O 329 8.00 N 314 7.00 C 1328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 251 " 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 81.7 milliseconds 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 490 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'E' and resid 27 through 55 removed outlier: 3.817A pdb=" N TYR E 54 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 93 through 126 removed outlier: 4.210A pdb=" N PHE E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Proline residue: E 105 - end of helix Processing helix chain 'E' and resid 126 through 132 Processing helix chain 'E' and resid 137 through 152 Processing helix chain 'E' and resid 178 through 204 Processing helix chain 'E' and resid 212 through 227 Processing helix chain 'E' and resid 229 through 242 Processing helix chain 'E' and resid 252 through 279 removed outlier: 3.929A pdb=" N VAL E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Proline residue: E 269 - end of helix removed outlier: 3.524A pdb=" N TYR E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 438 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: 0.31 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: 1.22 - 1.34: 577 1.34 - 1.46: 379 1.46 - 1.58: 1060 1.58 - 1.70: 3 1.70 - 1.82: 19 Bond restraints: 2038 Sorted by residual: bond pdb=" C12 JW0 E 601 " pdb=" C17 JW0 E 601 " ideal model delta sigma weight residual 1.545 1.460 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C10 JW0 E 601 " pdb=" C14 JW0 E 601 " ideal model delta sigma weight residual 1.538 1.463 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 JW0 E 601 " pdb=" C6 JW0 E 601 " ideal model delta sigma weight residual 1.538 1.467 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C15 JW0 E 601 " pdb=" C16 JW0 E 601 " ideal model delta sigma weight residual 1.549 1.607 -0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C7 JW0 E 601 " pdb=" C8 JW0 E 601 " ideal model delta sigma weight residual 1.532 1.474 0.058 2.00e-02 2.50e+03 8.44e+00 ... (remaining 2033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 2745 3.74 - 7.49: 42 7.49 - 11.23: 9 11.23 - 14.97: 3 14.97 - 18.72: 1 Bond angle restraints: 2800 Sorted by residual: angle pdb=" N VAL E 248 " pdb=" CA VAL E 248 " pdb=" C VAL E 248 " ideal model delta sigma weight residual 113.47 106.97 6.50 1.01e+00 9.80e-01 4.14e+01 angle pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" C VAL E 61 " ideal model delta sigma weight residual 113.71 108.13 5.58 9.50e-01 1.11e+00 3.45e+01 angle pdb=" CA LEU E 98 " pdb=" CB LEU E 98 " pdb=" CG LEU E 98 " ideal model delta sigma weight residual 116.30 135.02 -18.72 3.50e+00 8.16e-02 2.86e+01 angle pdb=" C12 JW0 E 601 " pdb=" C11 JW0 E 601 " pdb=" C9 JW0 E 601 " ideal model delta sigma weight residual 114.66 102.64 12.02 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CA LEU E 42 " pdb=" CB LEU E 42 " pdb=" CG LEU E 42 " ideal model delta sigma weight residual 116.30 129.58 -13.28 3.50e+00 8.16e-02 1.44e+01 ... (remaining 2795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1045 17.23 - 34.46: 148 34.46 - 51.69: 45 51.69 - 68.92: 2 68.92 - 86.15: 1 Dihedral angle restraints: 1241 sinusoidal: 488 harmonic: 753 Sorted by residual: dihedral pdb=" CA MET E 209 " pdb=" C MET E 209 " pdb=" N PRO E 210 " pdb=" CA PRO E 210 " ideal model delta harmonic sigma weight residual 180.00 143.71 36.29 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 251 " pdb=" CB CYS E 251 " ideal model delta sinusoidal sigma weight residual 93.00 132.97 -39.97 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB GLU E 157 " pdb=" CG GLU E 157 " pdb=" CD GLU E 157 " pdb=" OE1 GLU E 157 " ideal model delta sinusoidal sigma weight residual 0.00 -86.15 86.15 1 3.00e+01 1.11e-03 9.95e+00 ... (remaining 1238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 341 0.116 - 0.233: 12 0.233 - 0.349: 3 0.349 - 0.466: 1 0.466 - 0.582: 1 Chirality restraints: 358 Sorted by residual: chirality pdb=" C11 JW0 E 601 " pdb=" C12 JW0 E 601 " pdb=" C15 JW0 E 601 " pdb=" C9 JW0 E 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.95 0.58 2.00e-01 2.50e+01 8.47e+00 chirality pdb=" C17 JW0 E 601 " pdb=" C12 JW0 E 601 " pdb=" C16 JW0 E 601 " pdb=" C18 JW0 E 601 " both_signs ideal model delta sigma weight residual False 2.36 2.83 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C4 JW0 E 601 " pdb=" C3 JW0 E 601 " pdb=" C5 JW0 E 601 " pdb=" C7 JW0 E 601 " both_signs ideal model delta sigma weight residual False 2.39 2.67 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 355 not shown) Planarity restraints: 323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 209 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 210 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 134 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO E 135 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 172 " -0.012 2.00e-02 2.50e+03 1.19e-02 3.56e+00 pdb=" CG TRP E 172 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP E 172 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 172 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 172 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 172 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 172 " -0.000 2.00e-02 2.50e+03 ... (remaining 320 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 90 2.71 - 3.26: 2141 3.26 - 3.81: 3330 3.81 - 4.35: 3829 4.35 - 4.90: 6497 Nonbonded interactions: 15887 Sorted by model distance: nonbonded pdb=" OG SER E 100 " pdb=" NE1 TRP E 158 " model vdw 2.167 3.120 nonbonded pdb=" OH TYR E 106 " pdb=" O GLY E 229 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASN E 59 " pdb=" OG SER E 62 " model vdw 2.404 3.040 nonbonded pdb=" O LEU E 146 " pdb=" OG SER E 150 " model vdw 2.413 3.040 nonbonded pdb=" O GLY E 41 " pdb=" ND2 ASN E 45 " model vdw 2.440 3.120 ... (remaining 15882 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: 1.590 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.670 Find NCS groups from input model: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.006 0.085 2039 Z= 0.279 Angle : 1.162 18.717 2802 Z= 0.518 Chirality : 0.067 0.582 358 Planarity : 0.007 0.068 323 Dihedral : 16.896 86.151 748 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.47 % Allowed : 29.72 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % 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 are not related in a simple way. whole: 0.08 (0.56), residues: 251 helix: 1.26 (0.39), residues: 188 sheet: None (None), residues: 0 loop : -3.85 (0.66), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 58 TYR 0.019 0.002 TYR E 106 PHE 0.014 0.001 PHE E 104 TRP 0.032 0.002 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.28 ( 2038) covalent geometry : angle 1.16235 / 0.52 ( 2800) SS BOND : bond 0.00175 / 0.12 ( 1) SS BOND : angle 0.26377 / 0.18 ( 2) hydrogen bonds : bond 0.09988 / 6.32 ( 146) hydrogen bonds : angle 5.58074 / 3.97 ( 438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.096 Fit side-chains REVERT: E 24 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5419 (m-80) REVERT: E 97 ILE cc_start: 0.8421 (mm) cc_final: 0.8186 (mp) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0685 time to fit residues: 3.4808 Evaluate side-chains 44 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.137702 restraints weight = 3605.681| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.11 r_work: 0.3891 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2039 Z= 0.136 Angle : 0.735 8.500 2802 Z= 0.345 Chirality : 0.041 0.186 358 Planarity : 0.006 0.044 323 Dihedral : 8.097 49.844 353 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.77 % Allowed : 26.42 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % 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 are not related in a simple way. whole: 0.48 (0.56), residues: 251 helix: 1.55 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.89 (0.62), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.009 0.001 TYR E 254 PHE 0.012 0.001 PHE E 104 TRP 0.018 0.001 TRP E 172 HIS 0.003 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 2038) covalent geometry : angle 0.73481 / 0.35 ( 2800) SS BOND : bond 0.00206 / 0.14 ( 1) SS BOND : angle 0.13894 / 0.07 ( 2) hydrogen bonds : bond 0.04025 / 2.76 ( 146) hydrogen bonds : angle 4.47582 / 3.25 ( 438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.073 Fit side-chains REVERT: E 108 THR cc_start: 0.8421 (m) cc_final: 0.8050 (p) REVERT: E 131 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.6683 (mtt180) REVERT: E 172 TRP cc_start: 0.4217 (p-90) cc_final: 0.3998 (p-90) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.0732 time to fit residues: 4.6428 Evaluate side-chains 48 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135428 restraints weight = 3709.155| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.12 r_work: 0.3872 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2039 Z= 0.142 Angle : 0.734 9.699 2802 Z= 0.348 Chirality : 0.042 0.186 358 Planarity : 0.005 0.042 323 Dihedral : 7.296 31.890 351 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.57 % Favored : 92.03 % Rotamer: Outliers : 3.77 % Allowed : 27.83 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % 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 are not related in a simple way. whole: 0.34 (0.56), residues: 251 helix: 1.35 (0.39), residues: 194 sheet: None (None), residues: 0 loop : -3.91 (0.68), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 241 TYR 0.011 0.002 TYR E 240 PHE 0.009 0.001 PHE E 104 TRP 0.013 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 2038) covalent geometry : angle 0.73396 / 0.35 ( 2800) SS BOND : bond 0.00239 / 0.16 ( 1) SS BOND : angle 0.03873 / 0.03 ( 2) hydrogen bonds : bond 0.04056 / 2.76 ( 146) hydrogen bonds : angle 4.44459 / 3.22 ( 438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.079 Fit side-chains REVERT: E 108 THR cc_start: 0.8473 (m) cc_final: 0.8107 (p) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.0559 time to fit residues: 3.4624 Evaluate side-chains 52 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.153228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135800 restraints weight = 3611.592| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.19 r_work: 0.3875 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2039 Z= 0.132 Angle : 0.713 9.146 2802 Z= 0.337 Chirality : 0.042 0.170 358 Planarity : 0.005 0.043 323 Dihedral : 7.054 30.861 351 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.97 % Favored : 91.63 % Rotamer: Outliers : 4.25 % Allowed : 27.83 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % 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 are not related in a simple way. whole: 0.34 (0.55), residues: 251 helix: 1.44 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.89 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.011 0.001 TYR E 240 PHE 0.008 0.001 PHE E 104 TRP 0.006 0.001 TRP E 183 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 2038) covalent geometry : angle 0.71298 / 0.34 ( 2800) SS BOND : bond 0.00185 / 0.12 ( 1) SS BOND : angle 0.01200 / 0.01 ( 2) hydrogen bonds : bond 0.03908 / 2.69 ( 146) hydrogen bonds : angle 4.41699 / 3.20 ( 438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.081 Fit side-chains REVERT: E 97 ILE cc_start: 0.8451 (mm) cc_final: 0.8226 (mp) REVERT: E 108 THR cc_start: 0.8523 (m) cc_final: 0.8142 (p) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.0529 time to fit residues: 3.5895 Evaluate side-chains 55 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135696 restraints weight = 3628.619| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.11 r_work: 0.3876 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2039 Z= 0.135 Angle : 0.742 9.786 2802 Z= 0.349 Chirality : 0.043 0.232 358 Planarity : 0.005 0.043 323 Dihedral : 7.049 31.378 351 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.37 % Favored : 91.24 % Rotamer: Outliers : 7.08 % Allowed : 26.42 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.55), residues: 251 helix: 1.41 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.81 (0.62), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.011 0.001 TYR E 240 PHE 0.008 0.001 PHE E 104 TRP 0.017 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 2038) covalent geometry : angle 0.74232 / 0.35 ( 2800) SS BOND : bond 0.00173 / 0.12 ( 1) SS BOND : angle 0.03587 / 0.02 ( 2) hydrogen bonds : bond 0.03906 / 2.67 ( 146) hydrogen bonds : angle 4.50762 / 3.24 ( 438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.045 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.0495 time to fit residues: 3.0309 Evaluate side-chains 50 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.134237 restraints weight = 3636.750| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.16 r_work: 0.3859 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2039 Z= 0.141 Angle : 0.748 11.383 2802 Z= 0.350 Chirality : 0.043 0.222 358 Planarity : 0.005 0.043 323 Dihedral : 7.090 30.922 351 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.76 % Favored : 90.84 % Rotamer: Outliers : 5.19 % Allowed : 27.36 % Favored : 67.45 % 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 are not related in a simple way. whole: 0.27 (0.55), residues: 251 helix: 1.37 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.89 (0.60), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.010 0.001 TYR E 240 PHE 0.007 0.001 PHE E 104 TRP 0.018 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 2038) covalent geometry : angle 0.74808 / 0.35 ( 2800) SS BOND : bond 0.00178 / 0.12 ( 1) SS BOND : angle 0.10911 / 0.06 ( 2) hydrogen bonds : bond 0.04013 / 2.72 ( 146) hydrogen bonds : angle 4.51151 / 3.25 ( 438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.088 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 49 average time/residue: 0.0541 time to fit residues: 3.1119 Evaluate side-chains 53 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.133184 restraints weight = 3612.610| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.17 r_work: 0.3845 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2039 Z= 0.146 Angle : 0.753 12.190 2802 Z= 0.358 Chirality : 0.043 0.209 358 Planarity : 0.005 0.043 323 Dihedral : 7.127 30.568 351 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.97 % Favored : 91.63 % Rotamer: Outliers : 6.13 % Allowed : 25.94 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.55), residues: 251 helix: 1.32 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.86 (0.59), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.010 0.002 TYR E 240 PHE 0.008 0.001 PHE E 104 TRP 0.017 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 2038) covalent geometry : angle 0.75342 / 0.36 ( 2800) SS BOND : bond 0.00165 / 0.11 ( 1) SS BOND : angle 0.11587 / 0.07 ( 2) hydrogen bonds : bond 0.04104 / 2.79 ( 146) hydrogen bonds : angle 4.63694 / 3.39 ( 438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.083 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 48 average time/residue: 0.0595 time to fit residues: 3.3658 Evaluate side-chains 52 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132895 restraints weight = 3625.859| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.11 r_work: 0.3841 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2039 Z= 0.150 Angle : 0.781 12.814 2802 Z= 0.364 Chirality : 0.043 0.207 358 Planarity : 0.005 0.043 323 Dihedral : 7.168 30.631 351 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.37 % Favored : 91.24 % Rotamer: Outliers : 5.19 % Allowed : 27.36 % Favored : 67.45 % 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 are not related in a simple way. whole: 0.17 (0.55), residues: 251 helix: 1.28 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.81 (0.59), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.011 0.002 TYR E 240 PHE 0.007 0.001 PHE E 104 TRP 0.015 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 2038) covalent geometry : angle 0.78084 / 0.36 ( 2800) SS BOND : bond 0.00169 / 0.11 ( 1) SS BOND : angle 0.13841 / 0.08 ( 2) hydrogen bonds : bond 0.04152 / 2.83 ( 146) hydrogen bonds : angle 4.65670 / 3.41 ( 438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.076 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.0552 time to fit residues: 3.2698 Evaluate side-chains 51 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.135000 restraints weight = 3538.792| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.13 r_work: 0.3842 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2039 Z= 0.130 Angle : 0.756 13.597 2802 Z= 0.352 Chirality : 0.041 0.209 358 Planarity : 0.005 0.042 323 Dihedral : 6.926 31.809 351 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.97 % Favored : 91.63 % Rotamer: Outliers : 4.72 % Allowed : 27.83 % Favored : 67.45 % 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 are not related in a simple way. whole: 0.25 (0.55), residues: 251 helix: 1.35 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.81 (0.58), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 241 TYR 0.013 0.001 TYR E 240 PHE 0.005 0.001 PHE E 104 TRP 0.011 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 2038) covalent geometry : angle 0.75670 / 0.35 ( 2800) SS BOND : bond 0.00150 / 0.10 ( 1) SS BOND : angle 0.08653 / 0.06 ( 2) hydrogen bonds : bond 0.03964 / 2.71 ( 146) hydrogen bonds : angle 4.59666 / 3.37 ( 438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.072 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 46 average time/residue: 0.0576 time to fit residues: 3.1290 Evaluate side-chains 48 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.133760 restraints weight = 3652.256| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.18 r_work: 0.3820 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2039 Z= 0.146 Angle : 0.782 13.307 2802 Z= 0.365 Chirality : 0.042 0.207 358 Planarity : 0.005 0.042 323 Dihedral : 7.068 30.435 351 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.37 % Favored : 91.24 % Rotamer: Outliers : 4.25 % Allowed : 26.89 % Favored : 68.87 % 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 are not related in a simple way. whole: 0.28 (0.55), residues: 251 helix: 1.38 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.86 (0.57), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 241 TYR 0.011 0.002 TYR E 240 PHE 0.007 0.001 PHE E 104 TRP 0.012 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 2038) covalent geometry : angle 0.78275 / 0.36 ( 2800) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 0.18172 / 0.13 ( 2) hydrogen bonds : bond 0.04165 / 2.84 ( 146) hydrogen bonds : angle 4.61178 / 3.39 ( 438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.071 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 46 average time/residue: 0.0571 time to fit residues: 3.0955 Evaluate side-chains 50 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.0040 chunk 5 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.155082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137903 restraints weight = 3612.038| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.10 r_work: 0.3872 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2039 Z= 0.127 Angle : 0.772 13.832 2802 Z= 0.354 Chirality : 0.041 0.215 358 Planarity : 0.005 0.042 323 Dihedral : 6.793 32.726 351 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.57 % Favored : 92.03 % Rotamer: Outliers : 3.77 % Allowed : 28.30 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.55), residues: 251 helix: 1.46 (0.39), residues: 189 sheet: None (None), residues: 0 loop : -3.76 (0.58), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 241 TYR 0.014 0.001 TYR E 240 PHE 0.004 0.001 PHE E 104 TRP 0.009 0.001 TRP E 172 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2038) covalent geometry : angle 0.77253 / 0.35 ( 2800) SS BOND : bond 0.00070 / 0.05 ( 1) SS BOND : angle 0.17067 / 0.12 ( 2) hydrogen bonds : bond 0.03896 / 2.67 ( 146) hydrogen bonds : angle 4.58863 / 3.38 ( 438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 800.70 seconds wall clock time: 14 minutes 23.67 seconds (863.67 seconds total)