Starting phenix.real_space_refine on Fri Jul 3 21:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo1_26637/07_2026/7uo1_26637.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 7 Type Number sf(0) Gaussians Ca 10 9.91 5 P 454 5.49 5 S 2 5.16 5 C 4934 2.51 5 N 1993 2.21 5 O 3301 1.98 5 H 5894 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16588 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 12071 Classifications: {'RNA': 373} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 25, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128} Link IDs: {'rna2p': 51, 'rna3p': 321} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 2622 Classifications: {'RNA': 82} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 73} Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1885 Classifications: {'peptide': 112} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 46 residue: pdb=" P C B 20 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 31 " occ=0.00 ... (remaining 34 not shown) Time building chain proxies: 3.18, per 1000 atoms: 0.19 Number of scatterers: 16588 At special positions: 0 Unit cell: (99.6826, 116.048, 196.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 10 19.99 S 2 16.00 P 454 15.00 O 3301 8.00 N 1993 7.00 C 4934 6.00 H 5894 1.00 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: 1.37 Conformation dependent library (CDL) restraints added in 250.2 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 45.5% alpha, 13.4% beta 109 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.528A pdb=" N PHE A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 95 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 294 hydrogen bonds 544 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5893 1.03 - 1.22: 78 1.22 - 1.42: 5415 1.42 - 1.61: 6364 1.61 - 1.81: 11 Bond restraints: 17761 Sorted by residual: bond pdb=" C1' C B 35 " pdb=" N1 C B 35 " ideal model delta sigma weight residual 1.470 1.493 -0.023 1.50e-02 4.44e+03 2.39e+00 bond pdb=" C1' C B 131 " pdb=" N1 C B 131 " ideal model delta sigma weight residual 1.470 1.491 -0.021 1.50e-02 4.44e+03 1.90e+00 bond pdb=" C1' C B 343 " pdb=" N1 C B 343 " ideal model delta sigma weight residual 1.470 1.489 -0.019 1.50e-02 4.44e+03 1.60e+00 bond pdb=" C1' A C 14 " pdb=" N9 A C 14 " ideal model delta sigma weight residual 1.465 1.484 -0.019 1.50e-02 4.44e+03 1.58e+00 bond pdb=" C3' G B 64 " pdb=" O3' G B 64 " ideal model delta sigma weight residual 1.417 1.435 -0.018 1.50e-02 4.44e+03 1.41e+00 ... (remaining 17756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.92: 31738 17.92 - 35.84: 5 35.84 - 53.77: 0 53.77 - 71.69: 0 71.69 - 89.61: 42 Bond angle restraints: 31785 Sorted by residual: angle pdb=" O3' U B 299 " pdb=" P G B 300 " pdb=" OP1 G B 300 " ideal model delta sigma weight residual 108.00 18.39 89.61 3.00e+00 1.11e-01 8.92e+02 angle pdb=" O3' C B 9 " pdb=" P C B 10 " pdb=" OP1 C B 10 " ideal model delta sigma weight residual 108.00 18.82 89.18 3.00e+00 1.11e-01 8.84e+02 angle pdb=" O3' A B 13 " pdb=" P C B 14 " pdb=" OP1 C B 14 " ideal model delta sigma weight residual 108.00 18.84 89.16 3.00e+00 1.11e-01 8.83e+02 angle pdb=" O3' C C 75 " pdb=" P C C 76 " pdb=" OP1 C C 76 " ideal model delta sigma weight residual 108.00 19.12 88.88 3.00e+00 1.11e-01 8.78e+02 angle pdb=" O3' G B 19 " pdb=" P C B 20 " pdb=" OP1 C B 20 " ideal model delta sigma weight residual 108.00 19.22 88.78 3.00e+00 1.11e-01 8.76e+02 ... (remaining 31780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 6560 36.00 - 72.00: 427 72.00 - 108.00: 64 108.00 - 143.99: 53 143.99 - 179.99: 52 Dihedral angle restraints: 7156 sinusoidal: 6783 harmonic: 373 Sorted by residual: dihedral pdb=" C4' G B 101 " pdb=" C3' G B 101 " pdb=" C2' G B 101 " pdb=" C1' G B 101 " ideal model delta sinusoidal sigma weight residual -35.00 36.25 -71.25 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' A B 351 " pdb=" C3' A B 351 " pdb=" C2' A B 351 " pdb=" C1' A B 351 " ideal model delta sinusoidal sigma weight residual -35.00 36.20 -71.20 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G B 332 " pdb=" C3' G B 332 " pdb=" C2' G B 332 " pdb=" C1' G B 332 " ideal model delta sinusoidal sigma weight residual -35.00 35.79 -70.79 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 7153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2096 0.115 - 0.231: 83 0.231 - 0.346: 200 0.346 - 0.461: 23 0.461 - 0.577: 8 Chirality restraints: 2410 Sorted by residual: chirality pdb=" P A B 233 " pdb=" OP1 A B 233 " pdb=" OP2 A B 233 " pdb=" O5' A B 233 " both_signs ideal model delta sigma weight residual True 2.41 2.99 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" P C B 20 " pdb=" OP1 C B 20 " pdb=" OP2 C B 20 " pdb=" O5' C B 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" P C B 14 " pdb=" OP1 C B 14 " pdb=" OP2 C B 14 " pdb=" O5' C B 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 2407 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 35 " -0.030 2.00e-02 2.50e+03 1.54e-02 6.50e+00 pdb=" N1 C B 35 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C B 35 " -0.018 2.00e-02 2.50e+03 pdb=" O2 C B 35 " 0.019 2.00e-02 2.50e+03 pdb=" N3 C B 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B 35 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C B 35 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C B 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C B 35 " 0.003 2.00e-02 2.50e+03 pdb=" H5 C B 35 " -0.000 2.00e-02 2.50e+03 pdb=" H6 C B 35 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 106 " -0.008 2.00e-02 2.50e+03 1.18e-02 4.87e+00 pdb=" N9 G B 106 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G B 106 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 106 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 106 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 106 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G B 106 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 106 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 106 " 0.033 2.00e-02 2.50e+03 pdb=" N2 G B 106 " -0.022 2.00e-02 2.50e+03 pdb=" N3 G B 106 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 106 " -0.002 2.00e-02 2.50e+03 pdb=" H8 G B 106 " -0.003 2.00e-02 2.50e+03 pdb=" H1 G B 106 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 76 " -0.018 2.00e-02 2.50e+03 1.26e-02 4.37e+00 pdb=" N1 C C 76 " 0.018 2.00e-02 2.50e+03 pdb=" C2 C C 76 " -0.025 2.00e-02 2.50e+03 pdb=" O2 C C 76 " 0.019 2.00e-02 2.50e+03 pdb=" N3 C C 76 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 76 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C C 76 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C C 76 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 76 " 0.003 2.00e-02 2.50e+03 pdb=" H5 C C 76 " 0.002 2.00e-02 2.50e+03 pdb=" H6 C C 76 " 0.005 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1249 2.21 - 2.81: 22703 2.81 - 3.41: 39051 3.41 - 4.00: 52292 4.00 - 4.60: 76175 Nonbonded interactions: 191470 Sorted by model distance: nonbonded pdb=" O6 G B 52 " pdb=" H ARG A 6 " model vdw 1.615 2.450 nonbonded pdb="HO2' C B 138 " pdb=" O5' A B 139 " model vdw 1.618 2.450 nonbonded pdb="HO2' G B 84 " pdb=" O5' C B 85 " model vdw 1.632 2.450 nonbonded pdb=" H62 A B 81 " pdb=" O2' G B 280 " model vdw 1.635 2.450 nonbonded pdb="HO2' C B 35 " pdb=" OP2 C B 36 " model vdw 1.638 2.450 ... (remaining 191465 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=0.00 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.090 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.950 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 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 : 0.002 0.023 11867 Z= 0.154 Angle : 4.427 89.611 18304 Z= 1.518 Chirality : 0.099 0.577 2410 Planarity : 0.003 0.023 619 Dihedral : 27.215 179.992 5826 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.55 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: 0.03 (0.82), residues: 110 helix: 2.24 (0.74), residues: 46 sheet: -1.81 (0.82), residues: 30 loop : -1.24 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 56 PHE 0.003 0.000 PHE A 20 TRP 0.001 0.000 TRP A 107 HIS 0.002 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (11867) covalent geometry : angle 4.42697 / 1.52 (18304) hydrogen bonds : bond 0.07842 / 4.44 ( 339) hydrogen bonds : angle 3.08651 / 1.80 ( 670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7949 (mm) cc_final: 0.7600 (mm) REVERT: A 72 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6204 (tpt90) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2348 time to fit residues: 12.5538 Evaluate side-chains 34 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 = 0.4951 r_free = 0.4951 target = 0.276250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.249860 restraints weight = 48491.486| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 0.95 r_work: 0.4404 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11867 Z= 0.209 Angle : 1.898 31.380 18304 Z= 0.722 Chirality : 0.254 2.272 2410 Planarity : 0.005 0.045 619 Dihedral : 26.605 178.189 5581 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 12.24 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.85), residues: 110 helix: 2.26 (0.73), residues: 46 sheet: -1.18 (0.83), residues: 30 loop : -0.16 (1.34), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 97 PHE 0.010 0.002 PHE A 16 TRP 0.003 0.001 TRP A 107 HIS 0.005 0.002 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.21 (11867) covalent geometry : angle 1.89801 / 0.72 (18304) hydrogen bonds : bond 0.08175 / 4.80 ( 339) hydrogen bonds : angle 2.66390 / 1.52 ( 670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8081 (mt0) cc_final: 0.7878 (mt0) REVERT: A 72 ARG cc_start: 0.6386 (tpt90) cc_final: 0.4576 (tpt90) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.2318 time to fit residues: 11.1129 Evaluate side-chains 36 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.260729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.234267 restraints weight = 47702.698| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 1.47 r_work: 0.4175 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11867 Z= 0.258 Angle : 1.956 31.617 18304 Z= 0.729 Chirality : 0.239 2.097 2410 Planarity : 0.006 0.053 619 Dihedral : 26.748 179.704 5581 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.57 % 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: 0.40 (0.85), residues: 110 helix: 2.19 (0.75), residues: 46 sheet: -1.09 (0.97), residues: 21 loop : -1.15 (1.11), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 97 PHE 0.016 0.003 PHE A 4 TRP 0.004 0.002 TRP A 107 HIS 0.005 0.002 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.26 (11867) covalent geometry : angle 1.95602 / 0.73 (18304) hydrogen bonds : bond 0.08315 / 4.93 ( 339) hydrogen bonds : angle 3.16051 / 1.86 ( 670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.7783 (tt) cc_final: 0.7550 (tt) REVERT: A 72 ARG cc_start: 0.6705 (tpt90) cc_final: 0.4363 (tpt90) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.2374 time to fit residues: 10.3811 Evaluate side-chains 33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.4728 r_free = 0.4728 target = 0.249132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.205478 restraints weight = 38687.291| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 0.98 r_work: 0.4139 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11867 Z= 0.237 Angle : 1.894 29.247 18304 Z= 0.706 Chirality : 0.247 2.128 2410 Planarity : 0.006 0.033 619 Dihedral : 27.045 179.765 5581 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % Favored : 79.59 % 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: 0.19 (0.85), residues: 110 helix: 2.22 (0.76), residues: 46 sheet: -1.33 (0.88), residues: 21 loop : -1.46 (1.09), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 97 PHE 0.013 0.003 PHE A 4 TRP 0.006 0.002 TRP A 107 HIS 0.004 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.24 (11867) covalent geometry : angle 1.89407 / 0.71 (18304) hydrogen bonds : bond 0.08129 / 4.79 ( 339) hydrogen bonds : angle 3.20212 / 1.86 ( 670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 28 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6427 (tpt90) cc_final: 0.4021 (tpt90) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.2889 time to fit residues: 9.0373 Evaluate side-chains 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.245701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204984 restraints weight = 40453.176| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 0.84 r_work: 0.4164 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11867 Z= 0.231 Angle : 1.903 29.120 18304 Z= 0.707 Chirality : 0.244 2.100 2410 Planarity : 0.006 0.044 619 Dihedral : 27.073 179.903 5581 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.08 % Allowed : 18.37 % Favored : 77.55 % 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: 0.37 (0.87), residues: 110 helix: 2.33 (0.79), residues: 46 sheet: -1.09 (0.90), residues: 21 loop : -1.39 (1.12), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 97 PHE 0.011 0.003 PHE A 83 TRP 0.006 0.003 TRP A 107 HIS 0.005 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.23 (11867) covalent geometry : angle 1.90252 / 0.71 (18304) hydrogen bonds : bond 0.07993 / 4.69 ( 339) hydrogen bonds : angle 3.22970 / 1.90 ( 670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6402 (tpt90) cc_final: 0.4112 (tpt90) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.2763 time to fit residues: 10.0690 Evaluate side-chains 31 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 41 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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 = 0.4690 r_free = 0.4690 target = 0.243059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.201606 restraints weight = 39433.147| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.90 r_work: 0.4140 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.7726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11867 Z= 0.245 Angle : 1.901 29.191 18304 Z= 0.708 Chirality : 0.245 2.099 2410 Planarity : 0.006 0.035 619 Dihedral : 27.076 179.244 5581 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.06 % Allowed : 19.39 % Favored : 77.55 % 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: 0.14 (0.85), residues: 110 helix: 2.21 (0.78), residues: 46 sheet: -1.16 (0.91), residues: 21 loop : -1.64 (1.09), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 60 PHE 0.009 0.002 PHE A 18 TRP 0.005 0.002 TRP A 107 HIS 0.005 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.24 (11867) covalent geometry : angle 1.90119 / 0.71 (18304) hydrogen bonds : bond 0.08121 / 4.78 ( 339) hydrogen bonds : angle 3.31768 / 1.95 ( 670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6447 (tpt90) cc_final: 0.4173 (tpt90) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.2626 time to fit residues: 9.3489 Evaluate side-chains 29 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 10.9990 chunk 39 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.238766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.198637 restraints weight = 39932.527| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.29 r_work: 0.4055 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.8633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 11867 Z= 0.355 Angle : 1.980 30.826 18304 Z= 0.753 Chirality : 0.243 2.100 2410 Planarity : 0.007 0.069 619 Dihedral : 27.573 179.484 5581 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.08 % Allowed : 18.37 % Favored : 77.55 % 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: -0.96 (0.81), residues: 110 helix: 0.87 (0.72), residues: 46 sheet: -1.35 (0.93), residues: 21 loop : -1.90 (1.08), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 112 PHE 0.010 0.003 PHE A 71 TRP 0.009 0.003 TRP A 107 HIS 0.007 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.36 (11867) covalent geometry : angle 1.97976 / 0.75 (18304) hydrogen bonds : bond 0.10073 / 5.88 ( 339) hydrogen bonds : angle 3.93602 / 2.34 ( 670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6409 (tpt90) cc_final: 0.4089 (tpt90) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.2315 time to fit residues: 8.4861 Evaluate side-chains 31 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.238758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.198946 restraints weight = 40048.410| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.23 r_work: 0.4047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11867 Z= 0.343 Angle : 1.949 30.240 18304 Z= 0.735 Chirality : 0.244 2.095 2410 Planarity : 0.007 0.061 619 Dihedral : 27.568 177.572 5581 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.06 % Allowed : 18.37 % Favored : 78.57 % 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: -1.30 (0.78), residues: 110 helix: 0.54 (0.68), residues: 46 sheet: -1.45 (0.93), residues: 21 loop : -2.08 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 108 PHE 0.010 0.003 PHE A 71 TRP 0.009 0.004 TRP A 107 HIS 0.007 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.34 (11867) covalent geometry : angle 1.94910 / 0.74 (18304) hydrogen bonds : bond 0.09414 / 5.54 ( 339) hydrogen bonds : angle 3.76690 / 2.23 ( 670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6423 (tpt90) cc_final: 0.4095 (tpt90) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.2135 time to fit residues: 7.6995 Evaluate side-chains 29 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4638 r_free = 0.4638 target = 0.236070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196050 restraints weight = 39281.209| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.22 r_work: 0.4031 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.9369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 11867 Z= 0.394 Angle : 1.998 31.234 18304 Z= 0.763 Chirality : 0.243 2.082 2410 Planarity : 0.008 0.074 619 Dihedral : 27.903 179.276 5581 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.57 % 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: -1.93 (0.74), residues: 110 helix: -0.09 (0.65), residues: 46 sheet: -1.83 (0.92), residues: 21 loop : -2.22 (1.01), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 36 PHE 0.012 0.003 PHE A 71 TRP 0.009 0.004 TRP A 107 HIS 0.007 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.39 (11867) covalent geometry : angle 1.99753 / 0.76 (18304) hydrogen bonds : bond 0.10395 / 6.10 ( 339) hydrogen bonds : angle 4.07586 / 2.43 ( 670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6472 (tpt90) cc_final: 0.3985 (tpt90) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.2296 time to fit residues: 7.7845 Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.0670 chunk 11 optimal weight: 10.0000 overall best weight: 3.1924 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.241752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.202522 restraints weight = 39748.599| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.87 r_work: 0.4101 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.9042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11867 Z= 0.208 Angle : 1.894 28.593 18304 Z= 0.704 Chirality : 0.245 2.125 2410 Planarity : 0.006 0.045 619 Dihedral : 27.377 177.563 5581 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.06 % Allowed : 18.37 % Favored : 78.57 % 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: -0.65 (0.81), residues: 110 helix: 1.49 (0.71), residues: 46 sheet: -1.51 (0.95), residues: 21 loop : -2.02 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 108 PHE 0.008 0.002 PHE A 18 TRP 0.007 0.002 TRP A 107 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.21 (11867) covalent geometry : angle 1.89439 / 0.70 (18304) hydrogen bonds : bond 0.08043 / 4.74 ( 339) hydrogen bonds : angle 3.36917 / 1.98 ( 670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6314 (tpt90) cc_final: 0.4081 (tpt90) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.2293 time to fit residues: 8.0772 Evaluate side-chains 29 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 50.0000 chunk 21 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.237052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196729 restraints weight = 39716.953| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.25 r_work: 0.4035 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 11867 Z= 0.363 Angle : 1.970 30.725 18304 Z= 0.746 Chirality : 0.243 2.088 2410 Planarity : 0.007 0.064 619 Dihedral : 27.709 179.147 5581 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.06 % Allowed : 18.37 % Favored : 78.57 % 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: -1.48 (0.77), residues: 110 helix: 0.42 (0.67), residues: 46 sheet: -1.79 (0.94), residues: 21 loop : -2.05 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 108 PHE 0.012 0.003 PHE A 71 TRP 0.008 0.003 TRP A 107 HIS 0.008 0.003 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.36 (11867) covalent geometry : angle 1.96998 / 0.75 (18304) hydrogen bonds : bond 0.09874 / 5.78 ( 339) hydrogen bonds : angle 3.88730 / 2.31 ( 670) =============================================================================== Job complete usr+sys time: 3975.75 seconds wall clock time: 68 minutes 18.38 seconds (4098.38 seconds total)