Starting phenix.real_space_refine on Wed Aug 5 13:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zil_74278/08_2026/9zil_74278.map" } resolution = 3.1 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= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 36 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9945 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 19, 'rna3p_pur': 216, 'rna3p_pyr': 155} Link IDs: {'rna2p': 46, 'rna3p': 370} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Unusual residues: {' MG': 36} Classifications: {'undetermined': 36} Link IDs: {None: 35} Time building chain proxies: 2.41, per 1000 atoms: 0.24 Number of scatterers: 9945 At special positions: 0 Unit cell: (92.232, 174.948, 147.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 36 11.99 O 3051 8.00 N 1834 7.00 C 4604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 68.3 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 48.3% alpha, 15.5% beta 130 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.586A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.623A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.864A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 336 hydrogen bonds 586 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 953 1.33 - 1.45: 5330 1.45 - 1.57: 3878 1.57 - 1.69: 834 1.69 - 1.81: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C6 A A 155 " pdb=" N1 A A 155 " ideal model delta sigma weight residual 1.351 1.327 0.024 7.00e-03 2.04e+04 1.19e+01 bond pdb=" C6 A A 155 " pdb=" N6 A A 155 " ideal model delta sigma weight residual 1.335 1.308 0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C4 U A 171 " pdb=" O4 U A 171 " ideal model delta sigma weight residual 1.232 1.208 0.024 8.00e-03 1.56e+04 8.91e+00 bond pdb=" N3 U A 171 " pdb=" C4 U A 171 " ideal model delta sigma weight residual 1.380 1.355 0.025 9.00e-03 1.23e+04 7.43e+00 bond pdb=" N9 G A 172 " pdb=" C4 G A 172 " ideal model delta sigma weight residual 1.375 1.390 -0.015 8.00e-03 1.56e+04 3.42e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 16277 2.34 - 4.68: 652 4.68 - 7.02: 13 7.02 - 9.36: 0 9.36 - 11.71: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O4 U A 171 " pdb=" C4 U A 171 " pdb=" C5 U A 171 " ideal model delta sigma weight residual 125.90 136.44 -10.54 6.00e-01 2.78e+00 3.08e+02 angle pdb=" N3 U A 171 " pdb=" C4 U A 171 " pdb=" O4 U A 171 " ideal model delta sigma weight residual 119.40 107.69 11.71 7.00e-01 2.04e+00 2.80e+02 angle pdb=" N6 A A 155 " pdb=" C6 A A 155 " pdb=" N1 A A 155 " ideal model delta sigma weight residual 118.60 112.98 5.62 6.00e-01 2.78e+00 8.78e+01 angle pdb=" C2 U A 171 " pdb=" N3 U A 171 " pdb=" C4 U A 171 " ideal model delta sigma weight residual 127.00 130.63 -3.63 6.00e-01 2.78e+00 3.67e+01 angle pdb=" N1 U A 171 " pdb=" C2 U A 171 " pdb=" N3 U A 171 " ideal model delta sigma weight residual 114.90 111.35 3.55 6.00e-01 2.78e+00 3.50e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 5946 35.38 - 70.76: 1021 70.76 - 106.14: 142 106.14 - 141.52: 4 141.52 - 176.90: 3 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual 200.00 23.10 176.90 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -160.00 -82.65 -77.35 1 1.50e+01 4.44e-03 3.33e+01 dihedral pdb=" O4' A A 231 " pdb=" C1' A A 231 " pdb=" N9 A A 231 " pdb=" C4 A A 231 " ideal model delta sinusoidal sigma weight residual 254.00 171.24 82.76 1 1.70e+01 3.46e-03 2.90e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1540 0.043 - 0.086: 238 0.086 - 0.128: 154 0.128 - 0.171: 285 0.171 - 0.214: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' G A 173 " pdb=" C4' G A 173 " pdb=" O3' G A 173 " pdb=" C2' G A 173 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C2' C A 318 " pdb=" C3' C A 318 " pdb=" O2' C A 318 " pdb=" C1' C A 318 " both_signs ideal model delta sigma weight residual False -2.62 -2.82 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 171 " 0.007 2.00e-02 2.50e+03 1.73e-02 6.70e+00 pdb=" N1 U A 171 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U A 171 " 0.013 2.00e-02 2.50e+03 pdb=" O2 U A 171 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U A 171 " -0.024 2.00e-02 2.50e+03 pdb=" C4 U A 171 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U A 171 " 0.033 2.00e-02 2.50e+03 pdb=" C5 U A 171 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U A 171 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 194 " 0.006 2.00e-02 2.50e+03 1.67e-02 6.31e+00 pdb=" N1 C A 194 " -0.029 2.00e-02 2.50e+03 pdb=" C2 C A 194 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 194 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C A 194 " -0.019 2.00e-02 2.50e+03 pdb=" C4 C A 194 " 0.017 2.00e-02 2.50e+03 pdb=" N4 C A 194 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C A 194 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A 194 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.031 2.00e-02 2.50e+03 1.34e-02 5.39e+00 pdb=" N9 G A 298 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 38 2.55 - 3.13: 7088 3.13 - 3.72: 21370 3.72 - 4.31: 28018 4.31 - 4.90: 35433 Nonbonded interactions: 91947 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 510 " model vdw 1.958 2.170 nonbonded pdb=" OP2 G A 14 " pdb="MG MG A 506 " model vdw 1.965 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 507 " model vdw 1.982 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 510 " model vdw 2.003 2.170 nonbonded pdb=" O6 G A 299 " pdb="MG MG A 523 " model vdw 2.005 2.170 ... (remaining 91942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 10.390 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.240 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 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 : 0.003 0.041 11000 Z= 0.247 Angle : 0.856 11.705 16944 Z= 0.764 Chirality : 0.063 0.214 2221 Planarity : 0.004 0.025 581 Dihedral : 25.830 176.900 6900 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 1.01 % Allowed : 30.30 % Favored : 68.69 % 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: -0.16 (0.88), residues: 114 helix: 0.91 (0.80), residues: 53 sheet: -0.26 (1.09), residues: 26 loop : -1.45 (1.21), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.006 0.001 TYR B 81 PHE 0.003 0.001 PHE B 41 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.25 (11000) covalent geometry : angle 0.85632 / 0.76 (16944) hydrogen bonds : bond 0.08058 / 8.29 ( 385) hydrogen bonds : angle 3.30728 / 4.22 ( 724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.145 Fit side-chains REVERT: B 91 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7974 (pm20) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.0729 time to fit residues: 2.2765 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.096081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052685 restraints weight = 46091.692| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.75 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.119 11000 Z= 0.518 Angle : 0.949 11.328 16944 Z= 0.480 Chirality : 0.065 0.393 2221 Planarity : 0.007 0.044 581 Dihedral : 25.962 170.764 6648 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 9.09 % Allowed : 22.22 % Favored : 68.69 % 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: -0.59 (0.82), residues: 114 helix: 0.53 (0.70), residues: 53 sheet: -0.74 (1.04), residues: 26 loop : -1.35 (1.23), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 42 TYR 0.014 0.004 TYR B 81 PHE 0.015 0.004 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.52 (11000) covalent geometry : angle 0.94885 / 0.48 (16944) hydrogen bonds : bond 0.12295 / 13.11 ( 385) hydrogen bonds : angle 3.18578 / 4.08 ( 724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.190 Fit side-chains REVERT: B 91 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8030 (pm20) outliers start: 9 outliers final: 5 residues processed: 20 average time/residue: 0.0916 time to fit residues: 2.7311 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 overall best weight: 3.5984 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.096579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053506 restraints weight = 45699.231| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.08 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11000 Z= 0.296 Angle : 0.659 7.433 16944 Z= 0.362 Chirality : 0.047 0.388 2221 Planarity : 0.005 0.029 581 Dihedral : 26.019 172.396 6648 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % 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: -0.50 (0.84), residues: 114 helix: 0.76 (0.73), residues: 53 sheet: -0.78 (1.03), residues: 26 loop : -1.51 (1.21), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.014 0.003 TYR B 40 PHE 0.010 0.002 PHE B 68 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.30 (11000) covalent geometry : angle 0.65851 / 0.36 (16944) hydrogen bonds : bond 0.09101 / 9.57 ( 385) hydrogen bonds : angle 2.81698 / 3.56 ( 724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.139 Fit side-chains REVERT: B 91 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8032 (pm20) outliers start: 6 outliers final: 2 residues processed: 19 average time/residue: 0.0834 time to fit residues: 2.4930 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 12 optimal weight: 40.0000 chunk 45 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.095469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052909 restraints weight = 46170.906| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.30 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11000 Z= 0.385 Angle : 0.759 8.611 16944 Z= 0.404 Chirality : 0.053 0.379 2221 Planarity : 0.006 0.034 581 Dihedral : 26.030 168.180 6648 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % 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: -0.79 (0.82), residues: 114 helix: 0.55 (0.73), residues: 53 sheet: -0.91 (1.05), residues: 26 loop : -1.71 (1.15), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 42 TYR 0.016 0.003 TYR B 40 PHE 0.012 0.003 PHE B 17 HIS 0.008 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.39 (11000) covalent geometry : angle 0.75947 / 0.40 (16944) hydrogen bonds : bond 0.10421 / 11.00 ( 385) hydrogen bonds : angle 2.90176 / 3.69 ( 724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.159 Fit side-chains REVERT: B 91 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8289 (pm20) outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.0847 time to fit residues: 2.2615 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.094365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052896 restraints weight = 46589.065| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.30 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 11000 Z= 0.437 Angle : 0.856 9.214 16944 Z= 0.442 Chirality : 0.059 0.367 2221 Planarity : 0.006 0.045 581 Dihedral : 26.184 168.728 6648 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % 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: -0.97 (0.81), residues: 114 helix: 0.39 (0.73), residues: 53 sheet: -0.99 (1.05), residues: 26 loop : -1.79 (1.10), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.016 0.003 TYR B 40 PHE 0.020 0.004 PHE B 17 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.44 (11000) covalent geometry : angle 0.85554 / 0.44 (16944) hydrogen bonds : bond 0.11103 / 11.69 ( 385) hydrogen bonds : angle 3.01001 / 3.76 ( 724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.144 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 16 average time/residue: 0.0734 time to fit residues: 1.8752 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 50.0000 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.095497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052865 restraints weight = 45733.508| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.05 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11000 Z= 0.207 Angle : 0.579 7.347 16944 Z= 0.336 Chirality : 0.041 0.375 2221 Planarity : 0.005 0.028 581 Dihedral : 26.065 169.459 6645 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.03 % Allowed : 26.26 % Favored : 70.71 % 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: -0.40 (0.84), residues: 114 helix: 0.86 (0.75), residues: 53 sheet: -0.74 (1.08), residues: 26 loop : -1.49 (1.16), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.011 0.002 TYR B 31 PHE 0.016 0.002 PHE B 68 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.21 (11000) covalent geometry : angle 0.57889 / 0.34 (16944) hydrogen bonds : bond 0.08539 / 8.92 ( 385) hydrogen bonds : angle 2.63893 / 3.31 ( 724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.135 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 17 average time/residue: 0.0685 time to fit residues: 1.9585 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 overall best weight: 5.7586 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.093975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051592 restraints weight = 45796.221| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.68 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 11000 Z= 0.458 Angle : 0.853 9.573 16944 Z= 0.438 Chirality : 0.059 0.372 2221 Planarity : 0.006 0.036 581 Dihedral : 26.116 168.606 6645 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.03 % Allowed : 25.25 % Favored : 71.72 % 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: -0.84 (0.80), residues: 114 helix: 0.45 (0.72), residues: 53 sheet: -0.88 (1.06), residues: 26 loop : -1.70 (1.06), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.015 0.003 TYR B 40 PHE 0.013 0.003 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.46 (11000) covalent geometry : angle 0.85302 / 0.44 (16944) hydrogen bonds : bond 0.11272 / 11.86 ( 385) hydrogen bonds : angle 2.93770 / 3.69 ( 724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.175 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.0846 time to fit residues: 2.1240 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.092554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050196 restraints weight = 47011.375| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.42 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.116 11000 Z= 0.729 Angle : 1.229 14.967 16944 Z= 0.590 Chirality : 0.081 0.362 2221 Planarity : 0.007 0.052 581 Dihedral : 26.464 170.750 6645 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 33.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 24.24 % Favored : 71.72 % 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: -1.62 (0.77), residues: 114 helix: -0.33 (0.68), residues: 53 sheet: -0.89 (1.06), residues: 26 loop : -2.18 (1.05), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.026 0.005 TYR B 40 PHE 0.020 0.004 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01213 / 0.73 (11000) covalent geometry : angle 1.22919 / 0.59 (16944) hydrogen bonds : bond 0.15103 / 15.98 ( 385) hydrogen bonds : angle 3.36845 / 4.20 ( 724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.115 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.0654 time to fit residues: 1.6645 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 50.0000 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.094340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.051866 restraints weight = 45742.963| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 0.99 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11000 Z= 0.240 Angle : 0.684 8.462 16944 Z= 0.381 Chirality : 0.047 0.366 2221 Planarity : 0.005 0.027 581 Dihedral : 26.319 172.808 6645 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.02 % Allowed : 25.25 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.81), residues: 114 helix: 0.77 (0.74), residues: 53 sheet: -0.61 (0.99), residues: 26 loop : -1.92 (1.10), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.018 0.003 TYR B 5 PHE 0.018 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.24 (11000) covalent geometry : angle 0.68373 / 0.38 (16944) hydrogen bonds : bond 0.09546 / 10.04 ( 385) hydrogen bonds : angle 2.71038 / 3.36 ( 724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.142 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.0759 time to fit residues: 1.6761 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.092692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050243 restraints weight = 46609.144| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.96 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.095 11000 Z= 0.610 Angle : 1.077 12.835 16944 Z= 0.524 Chirality : 0.074 0.368 2221 Planarity : 0.007 0.046 581 Dihedral : 26.341 171.054 6645 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 28.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.02 % Allowed : 26.26 % Favored : 71.72 % 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: -1.26 (0.77), residues: 114 helix: 0.02 (0.69), residues: 53 sheet: -0.56 (1.01), residues: 26 loop : -2.23 (1.02), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.020 0.005 TYR B 40 PHE 0.015 0.004 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01017 / 0.61 (11000) covalent geometry : angle 1.07746 / 0.52 (16944) hydrogen bonds : bond 0.13163 / 13.87 ( 385) hydrogen bonds : angle 3.11491 / 3.89 ( 724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.139 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.0772 time to fit residues: 1.6979 Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.094348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052361 restraints weight = 45983.152| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 0.96 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11000 Z= 0.220 Angle : 0.625 7.831 16944 Z= 0.360 Chirality : 0.043 0.368 2221 Planarity : 0.005 0.025 581 Dihedral : 26.272 174.720 6645 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.01 % Allowed : 27.27 % Favored : 71.72 % 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: -0.39 (0.82), residues: 114 helix: 0.89 (0.74), residues: 53 sheet: -0.34 (0.99), residues: 26 loop : -1.90 (1.11), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.014 0.003 TYR B 5 PHE 0.016 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.22 (11000) covalent geometry : angle 0.62543 / 0.36 (16944) hydrogen bonds : bond 0.09214 / 9.68 ( 385) hydrogen bonds : angle 2.64609 / 3.31 ( 724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.40 seconds wall clock time: 54 minutes 28.24 seconds (3268.24 seconds total)