Starting phenix.real_space_refine on Thu Jul 2 19:40:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942.map" model { file = "/net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ows_70942/07_2026/9ows_70942_neut.cif" } resolution = 2.87 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= 0.012 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 22 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 5 residue(s): 0.00s 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: 9931 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': 28, 'rna2p_pyr': 15, 'rna3p_pur': 215, 'rna3p_pyr': 159} Link IDs: {'rna2p': 43, 'rna3p': 373} 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Time building chain proxies: 2.15, per 1000 atoms: 0.22 Number of scatterers: 9931 At special positions: 0 Unit cell: (143.078, 164.851, 100.57, 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 22 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: 0.89 Conformation dependent library (CDL) restraints added in 68.9 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: 4 helices and 1 sheets defined 43.1% alpha, 15.5% beta 138 base pairs and 230 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 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 49 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 230 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 851 1.32 - 1.44: 5142 1.44 - 1.56: 4170 1.56 - 1.68: 832 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.25e+01 bond pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.06e-02 8.90e+03 9.93e+00 bond pdb=" C ARG B 6 " pdb=" O ARG B 6 " ideal model delta sigma weight residual 1.235 1.203 0.031 1.22e-02 6.72e+03 6.65e+00 bond pdb=" P C A 123 " pdb=" O5' C A 123 " ideal model delta sigma weight residual 1.593 1.631 -0.038 1.50e-02 4.44e+03 6.33e+00 bond pdb=" N9 A A 290 " pdb=" C4 A A 290 " ideal model delta sigma weight residual 1.374 1.359 0.015 6.00e-03 2.78e+04 6.24e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14901 2.64 - 5.29: 1479 5.29 - 7.93: 536 7.93 - 10.58: 26 10.58 - 13.22: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' G A 299 " pdb=" P A A 300 " pdb=" O5' A A 300 " ideal model delta sigma weight residual 104.00 92.01 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" O3' G A 14 " pdb=" P G A 15 " pdb=" O5' G A 15 " ideal model delta sigma weight residual 104.00 93.96 10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" O3' A A 277 " pdb=" C3' A A 277 " pdb=" C2' A A 277 " ideal model delta sigma weight residual 109.50 99.69 9.81 1.50e+00 4.44e-01 4.28e+01 angle pdb=" N LYS B 4 " pdb=" CA LYS B 4 " pdb=" C LYS B 4 " ideal model delta sigma weight residual 111.03 104.99 6.04 1.11e+00 8.12e-01 2.96e+01 angle pdb=" C3' A A 263 " pdb=" O3' A A 263 " pdb=" P U A 264 " ideal model delta sigma weight residual 120.20 128.31 -8.11 1.50e+00 4.44e-01 2.93e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 5600 33.99 - 67.98: 1330 67.98 - 101.97: 176 101.97 - 135.97: 7 135.97 - 169.96: 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 30.04 169.96 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" CD ARG B 6 " pdb=" NE ARG B 6 " pdb=" CZ ARG B 6 " pdb=" NH1 ARG B 6 " ideal model delta sinusoidal sigma weight residual 0.00 -82.25 82.25 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" C5' G A 136 " pdb=" C4' G A 136 " pdb=" C3' G A 136 " pdb=" O3' G A 136 " ideal model delta sinusoidal sigma weight residual 147.00 95.89 51.11 1 8.00e+00 1.56e-02 5.58e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1273 0.113 - 0.227: 526 0.227 - 0.340: 59 0.340 - 0.453: 279 0.453 - 0.567: 84 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P G A 1 " pdb=" OP1 G A 1 " pdb=" OP2 G A 1 " pdb=" O5' G A 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" P C A 123 " pdb=" OP1 C A 123 " pdb=" OP2 C A 123 " pdb=" O5' C A 123 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" P A A 205 " pdb=" OP1 A A 205 " pdb=" OP2 A A 205 " pdb=" O5' A A 205 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.32e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 6 " 1.148 9.50e-02 1.11e+02 5.15e-01 1.59e+02 pdb=" NE ARG B 6 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B 6 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 6 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 6 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 8 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LYS B 8 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS B 8 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS B 9 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 0 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C GLY B 0 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY B 0 " 0.020 2.00e-02 2.50e+03 pdb=" N MET B 1 " 0.017 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 8 1.98 - 2.71: 1252 2.71 - 3.44: 14247 3.44 - 4.17: 39136 4.17 - 4.90: 44850 Nonbonded interactions: 99493 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="MG MG A 511 " model vdw 1.246 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 510 " model vdw 1.658 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 515 " model vdw 1.660 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 508 " model vdw 1.725 2.170 nonbonded pdb=" O3' G A 162 " pdb=" C5 C A 163 " model vdw 1.853 3.340 ... (remaining 99488 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.038 11000 Z= 0.726 Angle : 1.811 13.224 16944 Z= 1.035 Chirality : 0.201 0.567 2221 Planarity : 0.022 0.515 581 Dihedral : 28.745 169.958 6900 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 29.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 7.07 % Allowed : 38.38 % Favored : 54.55 % Cbeta Deviations : 0.93 % 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: -0.85 (0.80), residues: 114 helix: 0.59 (0.76), residues: 53 sheet: -1.20 (0.95), residues: 26 loop : -1.67 (1.05), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG B 106 TYR 0.009 0.001 TYR B 5 PHE 0.008 0.001 PHE B 17 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01092 / 0.73 (11000) covalent geometry : angle 1.81091 / 1.04 (16944) hydrogen bonds : bond 0.22442 / 22.46 ( 389) hydrogen bonds : angle 13.33556 / 15.70 ( 704) *********************** 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 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.139 Fit side-chains REVERT: B 11 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: B 12 GLU cc_start: 0.8203 (mp0) cc_final: 0.7789 (mt-10) REVERT: B 50 LYS cc_start: 0.8276 (mmtm) cc_final: 0.8016 (ptpp) REVERT: B 107 LYS cc_start: 0.8307 (tttt) cc_final: 0.8032 (tttt) outliers start: 7 outliers final: 0 residues processed: 41 average time/residue: 0.7113 time to fit residues: 30.9313 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.083874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050000 restraints weight = 47116.008| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.75 r_work: 0.2903 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11000 Z= 0.413 Angle : 0.784 9.877 16944 Z= 0.473 Chirality : 0.055 0.288 2221 Planarity : 0.008 0.110 581 Dihedral : 27.560 163.089 6648 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 8.08 % Allowed : 35.35 % Favored : 56.57 % 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: -0.90 (0.79), residues: 114 helix: 0.27 (0.77), residues: 53 sheet: -0.64 (0.93), residues: 26 loop : -1.74 (1.03), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 6 TYR 0.029 0.004 TYR B 31 PHE 0.019 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.41 (11000) covalent geometry : angle 0.78421 / 0.47 (16944) hydrogen bonds : bond 0.13225 / 11.86 ( 389) hydrogen bonds : angle 3.05749 / 3.63 ( 704) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.163 Fit side-chains REVERT: B 4 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (ttmt) REVERT: B 12 GLU cc_start: 0.8196 (mp0) cc_final: 0.7919 (mt-10) REVERT: B 83 ILE cc_start: 0.8710 (mp) cc_final: 0.8340 (mm) REVERT: B 84 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 107 LYS cc_start: 0.8627 (tttt) cc_final: 0.8365 (tttt) outliers start: 8 outliers final: 2 residues processed: 31 average time/residue: 0.8687 time to fit residues: 28.4027 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.083266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050345 restraints weight = 46961.011| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.16 r_work: 0.2860 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 11000 Z= 0.424 Angle : 0.705 8.247 16944 Z= 0.430 Chirality : 0.047 0.277 2221 Planarity : 0.007 0.046 581 Dihedral : 27.067 165.139 6645 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 9.09 % Allowed : 37.37 % Favored : 53.54 % 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: -0.93 (0.81), residues: 114 helix: 0.01 (0.76), residues: 52 sheet: -1.18 (0.88), residues: 26 loop : -0.79 (1.17), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.035 0.005 TYR B 31 PHE 0.026 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.42 (11000) covalent geometry : angle 0.70483 / 0.43 (16944) hydrogen bonds : bond 0.13412 / 11.50 ( 389) hydrogen bonds : angle 3.32394 / 4.13 ( 704) *********************** 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.147 Fit side-chains REVERT: B 4 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (ttmt) REVERT: B 12 GLU cc_start: 0.8528 (mp0) cc_final: 0.8318 (mt-10) REVERT: B 15 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8313 (mt-10) REVERT: B 32 THR cc_start: 0.8783 (m) cc_final: 0.8581 (t) REVERT: B 70 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7999 (mt-10) outliers start: 9 outliers final: 2 residues processed: 34 average time/residue: 0.8197 time to fit residues: 29.4260 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.083872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.049849 restraints weight = 47120.127| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.47 r_work: 0.2902 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11000 Z= 0.292 Angle : 0.596 7.970 16944 Z= 0.370 Chirality : 0.041 0.263 2221 Planarity : 0.006 0.048 581 Dihedral : 26.846 165.490 6645 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 44.44 % Favored : 51.52 % 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 (0.80), residues: 114 helix: -0.16 (0.73), residues: 54 sheet: -1.03 (0.90), residues: 26 loop : -0.75 (1.21), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.023 0.004 TYR B 31 PHE 0.012 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.29 (11000) covalent geometry : angle 0.59560 / 0.37 (16944) hydrogen bonds : bond 0.10497 / 8.58 ( 389) hydrogen bonds : angle 2.95762 / 3.70 ( 704) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.140 Fit side-chains REVERT: B 4 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8736 (ttmt) REVERT: B 15 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 1.0168 time to fit residues: 32.9613 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.082967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.050734 restraints weight = 46869.931| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.03 r_work: 0.2868 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11000 Z= 0.401 Angle : 0.672 7.902 16944 Z= 0.408 Chirality : 0.045 0.263 2221 Planarity : 0.006 0.050 581 Dihedral : 26.724 166.421 6645 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 8.08 % Allowed : 36.36 % Favored : 55.56 % 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: -1.24 (0.80), residues: 114 helix: -0.38 (0.73), residues: 53 sheet: -0.97 (0.94), residues: 25 loop : -1.06 (1.16), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.025 0.003 TYR B 31 PHE 0.015 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.40 (11000) covalent geometry : angle 0.67168 / 0.41 (16944) hydrogen bonds : bond 0.12738 / 10.89 ( 389) hydrogen bonds : angle 3.20259 / 3.96 ( 704) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.142 Fit side-chains REVERT: B 15 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 19 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8389 (mp10) outliers start: 8 outliers final: 2 residues processed: 31 average time/residue: 0.9085 time to fit residues: 29.5569 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.082792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049665 restraints weight = 47041.192| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.14 r_work: 0.2850 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11000 Z= 0.433 Angle : 0.679 7.900 16944 Z= 0.412 Chirality : 0.046 0.260 2221 Planarity : 0.006 0.053 581 Dihedral : 26.711 166.306 6645 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 3.03 % Allowed : 41.41 % Favored : 55.56 % 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: -1.31 (0.80), residues: 114 helix: -0.44 (0.72), residues: 54 sheet: -1.49 (0.90), residues: 26 loop : -0.64 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.024 0.004 TYR B 31 PHE 0.012 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.43 (11000) covalent geometry : angle 0.67904 / 0.41 (16944) hydrogen bonds : bond 0.11981 / 10.08 ( 389) hydrogen bonds : angle 3.18110 / 3.93 ( 704) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: B 15 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8283 (mt-10) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.7561 time to fit residues: 25.5443 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.083221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050209 restraints weight = 46710.780| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.59 r_work: 0.2883 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11000 Z= 0.310 Angle : 0.605 7.889 16944 Z= 0.374 Chirality : 0.041 0.248 2221 Planarity : 0.006 0.044 581 Dihedral : 26.638 166.157 6645 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 44.44 % Favored : 51.52 % 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: -1.18 (0.80), residues: 114 helix: -0.32 (0.76), residues: 53 sheet: -1.36 (0.93), residues: 26 loop : -0.64 (1.11), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.021 0.003 TYR B 31 PHE 0.006 0.001 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.31 (11000) covalent geometry : angle 0.60481 / 0.37 (16944) hydrogen bonds : bond 0.10939 / 9.06 ( 389) hydrogen bonds : angle 3.04915 / 3.76 ( 704) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 15 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8222 (mt-10) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.7446 time to fit residues: 25.0955 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.082470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050482 restraints weight = 46546.445| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.40 r_work: 0.2850 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11000 Z= 0.472 Angle : 0.710 7.732 16944 Z= 0.426 Chirality : 0.047 0.258 2221 Planarity : 0.007 0.056 581 Dihedral : 26.584 166.293 6645 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.03 % Allowed : 50.51 % Favored : 46.46 % 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: -1.51 (0.80), residues: 114 helix: -0.70 (0.73), residues: 53 sheet: -1.55 (0.91), residues: 26 loop : -0.57 (1.14), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.023 0.003 TYR B 31 PHE 0.009 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.47 (11000) covalent geometry : angle 0.71038 / 0.43 (16944) hydrogen bonds : bond 0.12557 / 10.69 ( 389) hydrogen bonds : angle 3.24065 / 3.98 ( 704) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.091 Fit side-chains REVERT: B 15 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 19 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8409 (mp10) outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.6928 time to fit residues: 22.5905 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.083180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051577 restraints weight = 46683.861| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.67 r_work: 0.2882 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11000 Z= 0.333 Angle : 0.621 8.125 16944 Z= 0.382 Chirality : 0.041 0.241 2221 Planarity : 0.006 0.048 581 Dihedral : 26.592 165.976 6645 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 9.09 % Allowed : 43.43 % Favored : 47.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -1.34 (0.80), residues: 114 helix: -0.52 (0.75), residues: 53 sheet: -1.43 (0.94), residues: 26 loop : -0.60 (1.13), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.022 0.003 TYR B 31 PHE 0.008 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.33 (11000) covalent geometry : angle 0.62079 / 0.38 (16944) hydrogen bonds : bond 0.11077 / 9.20 ( 389) hydrogen bonds : angle 3.09930 / 3.80 ( 704) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.135 Fit side-chains REVERT: B 15 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8156 (mt-10) REVERT: B 19 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: B 113 LYS cc_start: 0.8453 (tppt) cc_final: 0.8246 (tppt) outliers start: 9 outliers final: 2 residues processed: 35 average time/residue: 0.6201 time to fit residues: 22.9483 Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.082712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050092 restraints weight = 46600.424| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.05 r_work: 0.2862 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11000 Z= 0.384 Angle : 0.656 8.573 16944 Z= 0.400 Chirality : 0.043 0.236 2221 Planarity : 0.006 0.053 581 Dihedral : 26.521 165.692 6645 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 48.48 % Favored : 46.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -1.46 (0.79), residues: 114 helix: -0.61 (0.73), residues: 53 sheet: -1.39 (0.94), residues: 26 loop : -0.78 (1.13), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.021 0.003 TYR B 31 PHE 0.008 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.38 (11000) covalent geometry : angle 0.65620 / 0.40 (16944) hydrogen bonds : bond 0.11913 / 10.05 ( 389) hydrogen bonds : angle 3.21141 / 3.89 ( 704) ********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.126 Fit side-chains REVERT: B 15 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8187 (mt-10) outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.5872 time to fit residues: 21.1785 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.082733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.050549 restraints weight = 47216.618| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.93 r_work: 0.2874 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11000 Z= 0.371 Angle : 0.642 7.922 16944 Z= 0.392 Chirality : 0.043 0.220 2221 Planarity : 0.006 0.049 581 Dihedral : 26.507 164.926 6645 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 6.06 % Allowed : 47.47 % Favored : 46.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -1.13 (0.82), residues: 114 helix: -0.20 (0.76), residues: 53 sheet: -1.48 (0.94), residues: 26 loop : -0.63 (1.18), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.023 0.003 TYR B 31 PHE 0.010 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.37 (11000) covalent geometry : angle 0.64173 / 0.39 (16944) hydrogen bonds : bond 0.11143 / 9.25 ( 389) hydrogen bonds : angle 3.29858 / 3.87 ( 704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.73 seconds wall clock time: 68 minutes 31.72 seconds (4111.72 seconds total)