Starting phenix.real_space_refine on Wed Aug 5 13:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ows_70942/08_2026/9ows_70942_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ows_70942/08_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_70942/08_2026/9ows_70942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ows_70942/08_2026/9ows_70942.map" model { file = "/net/cci-nas-00/data/ceres_data/9ows_70942/08_2026/9ows_70942_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ows_70942/08_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-2.2rc3-6140/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: 1.91, per 1000 atoms: 0.19 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: 0.77 Conformation dependent library (CDL) restraints added in 45.9 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: 1.95 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: 2.27 Time building geometry restraints manager: 1.04 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=" P C A 123 " pdb=" O5' C A 123 " ideal model delta sigma weight residual 1.593 1.631 -0.038 1.00e-02 1.00e+04 1.42e+01 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=" P G A 338 " pdb=" O5' G A 338 " ideal model delta sigma weight residual 1.593 1.561 0.032 1.00e-02 1.00e+04 1.05e+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=" P G A 128 " pdb=" O5' G A 128 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.26e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 15120 2.64 - 5.29: 1260 5.29 - 7.93: 536 7.93 - 10.58: 26 10.58 - 13.22: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" C3' A A 263 " pdb=" O3' A A 263 " pdb=" P U A 264 " ideal model delta sigma weight residual 119.70 128.31 -8.61 1.20e+00 6.94e-01 5.15e+01 angle pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " ideal model delta sigma weight residual 108.50 112.92 -4.42 7.00e-01 2.04e+00 3.99e+01 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 1.90e+00 2.77e-01 3.98e+01 angle pdb=" C4' A A 389 " pdb=" O4' A A 389 " pdb=" C1' A A 389 " ideal model delta sigma weight residual 109.70 105.38 4.32 7.00e-01 2.04e+00 3.80e+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 ... (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: 1415 0.113 - 0.227: 384 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: 5.540 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 11.470 Find NCS groups from input model: 0.040 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- 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= 0.799 Angle : 1.744 13.224 16944 Z= 0.998 Chirality : 0.196 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 0.01100 / 0.80 (11000) covalent geometry : angle 1.74375 / 1.00 (16944) hydrogen bonds : bond 0.22442 / 24.21 ( 389) hydrogen bonds : angle 13.33556 / 16.45 ( 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 : 0.134 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: 0.7790 (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: 0.6345 time to fit residues: 27.6465 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 : 0.082 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 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 = 0.4060 r_free = 0.4060 target = 0.083756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.050311 restraints weight = 46997.314| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.56 r_work: 0.2877 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11000 Z= 0.411 Angle : 0.938 9.735 16944 Z= 0.496 Chirality : 0.064 0.358 2221 Planarity : 0.008 0.117 581 Dihedral : 27.385 164.098 6648 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 7.07 % Allowed : 35.35 % Favored : 57.58 % 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: -0.95 (0.79), residues: 114 helix: 0.25 (0.76), residues: 53 sheet: -0.68 (0.93), residues: 26 loop : -1.80 (1.03), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 6 TYR 0.030 0.004 TYR B 31 PHE 0.021 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.41 (11000) covalent geometry : angle 0.93750 / 0.50 (16944) hydrogen bonds : bond 0.13531 / 13.51 ( 389) hydrogen bonds : angle 3.20598 / 4.15 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.134 Fit side-chains REVERT: B 4 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (ttmt) REVERT: B 12 GLU cc_start: 0.8211 (mp0) cc_final: 0.7930 (mt-10) REVERT: B 84 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 107 LYS cc_start: 0.8628 (tttt) cc_final: 0.8357 (tttt) outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.7601 time to fit residues: 24.0861 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.082616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049045 restraints weight = 46921.996| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.55 r_work: 0.2833 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 11000 Z= 0.522 Angle : 0.974 14.890 16944 Z= 0.510 Chirality : 0.063 0.354 2221 Planarity : 0.008 0.054 581 Dihedral : 27.053 167.126 6645 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 13.13 % Allowed : 33.33 % 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: -1.42 (0.77), residues: 114 helix: -0.50 (0.73), residues: 53 sheet: -1.25 (0.83), residues: 26 loop : -1.01 (1.11), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 62 TYR 0.042 0.005 TYR B 31 PHE 0.030 0.005 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.52 (11000) covalent geometry : angle 0.97405 / 0.51 (16944) hydrogen bonds : bond 0.15432 / 15.47 ( 389) hydrogen bonds : angle 3.61370 / 4.81 ( 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.144 Fit side-chains REVERT: B 4 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8664 (ttmt) REVERT: B 6 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8340 (mtt180) REVERT: B 12 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: B 15 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 26 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8161 (tpp80) REVERT: B 32 THR cc_start: 0.8836 (m) cc_final: 0.8530 (t) REVERT: B 59 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8946 (ttp80) REVERT: B 111 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7860 (mt) outliers start: 13 outliers final: 2 residues processed: 36 average time/residue: 0.7832 time to fit residues: 29.7648 Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 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 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 75 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 50 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 37 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 10.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.083874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.051245 restraints weight = 47222.292| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 0.97 r_work: 0.2893 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11000 Z= 0.266 Angle : 0.679 8.191 16944 Z= 0.390 Chirality : 0.045 0.310 2221 Planarity : 0.006 0.050 581 Dihedral : 26.802 167.170 6645 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.03 % Allowed : 39.39 % Favored : 57.58 % 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: -1.22 (0.79), residues: 114 helix: -0.29 (0.74), residues: 53 sheet: -1.30 (0.84), residues: 26 loop : -0.86 (1.19), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.022 0.003 TYR B 31 PHE 0.009 0.001 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.27 (11000) covalent geometry : angle 0.67892 / 0.39 (16944) hydrogen bonds : bond 0.11290 / 10.91 ( 389) hydrogen bonds : angle 3.11813 / 4.16 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.143 Fit side-chains REVERT: B 15 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 19 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: B 26 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7916 (tpp80) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.7338 time to fit residues: 23.1588 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 19 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.082707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050599 restraints weight = 46999.124| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.52 r_work: 0.2852 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.4011 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= 0.456 Angle : 0.870 11.516 16944 Z= 0.461 Chirality : 0.057 0.331 2221 Planarity : 0.007 0.057 581 Dihedral : 26.626 167.979 6645 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 41.41 % Favored : 52.53 % 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: -1.45 (0.81), residues: 114 helix: -0.70 (0.72), residues: 54 sheet: -1.51 (0.85), residues: 26 loop : -0.45 (1.29), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.027 0.003 TYR B 31 PHE 0.015 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.46 (11000) covalent geometry : angle 0.87040 / 0.46 (16944) hydrogen bonds : bond 0.13498 / 13.47 ( 389) hydrogen bonds : angle 3.28913 / 4.39 ( 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.151 Fit side-chains REVERT: B 6 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8303 (mtt180) REVERT: B 15 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 59 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8775 (ttp80) outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.7775 time to fit residues: 27.8169 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 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: 30.0000 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 = 0.082251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.049846 restraints weight = 47248.954| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.57 r_work: 0.2837 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 11000 Z= 0.514 Angle : 0.961 12.668 16944 Z= 0.502 Chirality : 0.063 0.377 2221 Planarity : 0.007 0.048 581 Dihedral : 26.675 168.511 6645 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 10.10 % Allowed : 36.36 % 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: -1.90 (0.78), residues: 114 helix: -0.87 (0.70), residues: 54 sheet: -2.35 (0.75), residues: 26 loop : -0.45 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 26 TYR 0.030 0.004 TYR B 31 PHE 0.016 0.003 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.51 (11000) covalent geometry : angle 0.96077 / 0.50 (16944) hydrogen bonds : bond 0.14555 / 14.85 ( 389) hydrogen bonds : angle 3.72954 / 4.91 ( 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8400 (mtt180) REVERT: B 14 GLN cc_start: 0.8920 (mm110) cc_final: 0.8673 (mm-40) REVERT: B 15 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 19 GLN cc_start: 0.8895 (mp10) cc_final: 0.8131 (mp10) REVERT: B 34 ASP cc_start: 0.8311 (t0) cc_final: 0.8108 (t0) REVERT: B 59 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8922 (ttp80) REVERT: B 80 ASP cc_start: 0.8076 (p0) cc_final: 0.7658 (p0) outliers start: 10 outliers final: 4 residues processed: 37 average time/residue: 0.7332 time to fit residues: 28.6701 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 : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 11.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.082771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049423 restraints weight = 46954.474| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.31 r_work: 0.2859 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11000 Z= 0.361 Angle : 0.762 9.428 16944 Z= 0.420 Chirality : 0.051 0.319 2221 Planarity : 0.006 0.054 581 Dihedral : 26.593 167.910 6645 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: -1.31 (0.79), residues: 114 helix: -0.34 (0.73), residues: 54 sheet: -2.11 (0.80), residues: 26 loop : -0.23 (1.20), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.025 0.003 TYR B 31 PHE 0.009 0.002 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.36 (11000) covalent geometry : angle 0.76174 / 0.42 (16944) hydrogen bonds : bond 0.12209 / 12.23 ( 389) hydrogen bonds : angle 3.35792 / 4.48 ( 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.145 Fit side-chains REVERT: B 15 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 59 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8772 (ttp80) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.7554 time to fit residues: 27.9674 Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.082440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050839 restraints weight = 46655.833| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.52 r_work: 0.2839 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11000 Z= 0.448 Angle : 0.871 11.017 16944 Z= 0.462 Chirality : 0.057 0.329 2221 Planarity : 0.007 0.054 581 Dihedral : 26.522 167.641 6645 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.08 % Allowed : 43.43 % Favored : 48.48 % 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: -1.64 (0.77), residues: 114 helix: -0.68 (0.70), residues: 54 sheet: -2.04 (0.82), residues: 26 loop : -0.47 (1.15), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.025 0.003 TYR B 31 PHE 0.012 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.45 (11000) covalent geometry : angle 0.87098 / 0.46 (16944) hydrogen bonds : bond 0.13696 / 13.96 ( 389) hydrogen bonds : angle 3.47219 / 4.58 ( 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 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.136 Fit side-chains REVERT: B 15 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 19 GLN cc_start: 0.8829 (mp10) cc_final: 0.8088 (mp10) REVERT: B 59 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8769 (ttp80) REVERT: B 113 LYS cc_start: 0.8505 (tppt) cc_final: 0.8264 (tppt) outliers start: 8 outliers final: 3 residues processed: 33 average time/residue: 0.7349 time to fit residues: 25.5600 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.083166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051360 restraints weight = 46620.963| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 0.99 r_work: 0.2892 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11000 Z= 0.284 Angle : 0.676 8.603 16944 Z= 0.383 Chirality : 0.044 0.282 2221 Planarity : 0.006 0.049 581 Dihedral : 26.441 167.161 6645 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.03 % Allowed : 49.49 % Favored : 47.47 % 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: -1.14 (0.80), residues: 114 helix: -0.16 (0.74), residues: 54 sheet: -1.65 (0.91), residues: 26 loop : -0.57 (1.15), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.021 0.002 TYR B 31 PHE 0.014 0.002 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.28 (11000) covalent geometry : angle 0.67596 / 0.38 (16944) hydrogen bonds : bond 0.11069 / 11.03 ( 389) hydrogen bonds : angle 3.20748 / 4.26 ( 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.138 Fit side-chains REVERT: B 15 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 59 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8708 (ttp80) outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.7700 time to fit residues: 26.0588 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.082286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.050624 restraints weight = 46700.583| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.56 r_work: 0.2837 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 11000 Z= 0.467 Angle : 0.856 10.933 16944 Z= 0.454 Chirality : 0.057 0.314 2221 Planarity : 0.007 0.056 581 Dihedral : 26.399 167.018 6645 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 47.47 % Favored : 47.47 % 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: -1.55 (0.78), residues: 114 helix: -0.58 (0.71), residues: 54 sheet: -1.81 (0.87), residues: 26 loop : -0.64 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 42 TYR 0.024 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 0.00718 / 0.47 (11000) covalent geometry : angle 0.85610 / 0.45 (16944) hydrogen bonds : bond 0.13471 / 13.81 ( 389) hydrogen bonds : angle 3.39332 / 4.45 ( 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.153 Fit side-chains REVERT: B 15 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 59 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8738 (ttp80) REVERT: B 96 GLU cc_start: 0.7782 (mp0) cc_final: 0.7545 (pm20) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.8274 time to fit residues: 27.0149 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 : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.082517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050001 restraints weight = 47327.321| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.39 r_work: 0.2855 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11000 Z= 0.388 Angle : 0.778 10.300 16944 Z= 0.423 Chirality : 0.052 0.294 2221 Planarity : 0.006 0.051 581 Dihedral : 26.392 166.498 6645 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 48.48 % Favored : 47.47 % 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: -1.35 (0.80), residues: 114 helix: -0.35 (0.73), residues: 54 sheet: -1.78 (0.88), residues: 26 loop : -0.61 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 42 TYR 0.023 0.003 TYR B 31 PHE 0.013 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.39 (11000) covalent geometry : angle 0.77822 / 0.42 (16944) hydrogen bonds : bond 0.12279 / 12.52 ( 389) hydrogen bonds : angle 3.34593 / 4.40 ( 704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.48 seconds wall clock time: 69 minutes 18.15 seconds (4158.15 seconds total)