Starting phenix.real_space_refine on Thu Jul 2 22:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo0_26636/07_2026/7uo0_26636.map" } resolution = 3.4 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= 0.013 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 Ca 7 9.91 5 P 454 5.49 5 S 2 5.16 5 C 4935 2.51 5 N 1996 2.21 5 O 3303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10697 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 8024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 8024 Classifications: {'RNA': 373} Modifications used: {'5*END': 1, 'rna2p_pur': 27, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128} Link IDs: {'rna2p': 53, 'rna3p': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1744 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 37, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 70} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 47 residue: pdb=" P C B 20 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 31 " occ=0.00 ... (remaining 35 not shown) Time building chain proxies: 2.45, per 1000 atoms: 0.23 Number of scatterers: 10697 At special positions: 0 Unit cell: (125.902, 115.322, 194.672, 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) Ca 7 19.99 S 2 16.00 P 454 15.00 O 3303 8.00 N 1996 7.00 C 4935 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: 0.84 Conformation dependent library (CDL) restraints added in 93.0 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 40.2% alpha, 11.6% beta 113 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.778A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 96 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.739A pdb=" N GLY A 36 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 27 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 113 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1461 1.33 - 1.45: 5697 1.45 - 1.57: 3806 1.57 - 1.69: 907 1.69 - 1.81: 3 Bond restraints: 11874 Sorted by residual: bond pdb=" C3' G C 19 " pdb=" O3' G C 19 " ideal model delta sigma weight residual 1.417 1.440 -0.023 1.50e-02 4.44e+03 2.27e+00 bond pdb=" C1' C B 35 " pdb=" N1 C B 35 " ideal model delta sigma weight residual 1.470 1.492 -0.022 1.50e-02 4.44e+03 2.14e+00 bond pdb=" C3' G B 137 " pdb=" O3' G B 137 " ideal model delta sigma weight residual 1.417 1.438 -0.021 1.50e-02 4.44e+03 2.04e+00 bond pdb=" C1' G B 190 " pdb=" N9 G B 190 " ideal model delta sigma weight residual 1.465 1.486 -0.021 1.50e-02 4.44e+03 2.03e+00 bond pdb=" C3' A B 352 " pdb=" O3' A B 352 " ideal model delta sigma weight residual 1.417 1.438 -0.021 1.50e-02 4.44e+03 1.96e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.47: 18310 15.47 - 30.94: 4 30.94 - 46.41: 0 46.41 - 61.88: 0 61.88 - 77.35: 5 Bond angle restraints: 18319 Sorted by residual: angle pdb=" O3' C B 14 " pdb=" P A B 15 " pdb=" OP1 A B 15 " ideal model delta sigma weight residual 108.00 30.65 77.35 3.00e+00 1.11e-01 6.65e+02 angle pdb=" O3' A B 15 " pdb=" P G B 16 " pdb=" OP1 G B 16 " ideal model delta sigma weight residual 108.00 34.51 73.49 3.00e+00 1.11e-01 6.00e+02 angle pdb=" O3' A B 130 " pdb=" P C B 131 " pdb=" OP1 C B 131 " ideal model delta sigma weight residual 108.00 34.71 73.29 3.00e+00 1.11e-01 5.97e+02 angle pdb=" O3' C B 70 " pdb=" P C B 71 " pdb=" OP1 C B 71 " ideal model delta sigma weight residual 108.00 35.06 72.94 3.00e+00 1.11e-01 5.91e+02 angle pdb=" O3' C B 252 " pdb=" P C B 253 " pdb=" OP1 C B 253 " ideal model delta sigma weight residual 108.00 36.18 71.82 3.00e+00 1.11e-01 5.73e+02 ... (remaining 18314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 5466 35.89 - 71.77: 452 71.77 - 107.66: 63 107.66 - 143.55: 28 143.55 - 179.43: 31 Dihedral angle restraints: 6040 sinusoidal: 5715 harmonic: 325 Sorted by residual: dihedral pdb=" C4' C C 63 " pdb=" C3' C C 63 " pdb=" C2' C C 63 " pdb=" C1' C C 63 " ideal model delta sinusoidal sigma weight residual -35.00 36.41 -71.41 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G B 190 " pdb=" C3' G B 190 " pdb=" C2' G B 190 " pdb=" C1' G B 190 " ideal model delta sinusoidal sigma weight residual -35.00 36.38 -71.38 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' C C 49 " pdb=" C3' C C 49 " pdb=" C2' C C 49 " pdb=" C1' C C 49 " ideal model delta sinusoidal sigma weight residual -35.00 35.89 -70.89 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2098 0.180 - 0.360: 286 0.360 - 0.540: 22 0.540 - 0.721: 2 0.721 - 0.901: 4 Chirality restraints: 2412 Sorted by residual: chirality pdb=" P C B 253 " pdb=" OP1 C B 253 " pdb=" OP2 C B 253 " pdb=" O5' C B 253 " both_signs ideal model delta sigma weight residual True 2.41 1.51 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" P C B 71 " pdb=" OP1 C B 71 " pdb=" OP2 C B 71 " pdb=" O5' C B 71 " both_signs ideal model delta sigma weight residual True 2.41 1.52 0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" P C B 131 " pdb=" OP1 C B 131 " pdb=" OP2 C B 131 " pdb=" O5' C B 131 " both_signs ideal model delta sigma weight residual True 2.41 1.58 0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 2409 not shown) Planarity restraints: 619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 35 " -0.001 2.00e-02 2.50e+03 1.40e-02 4.43e+00 pdb=" N1 C B 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C B 35 " 0.034 2.00e-02 2.50e+03 pdb=" O2 C B 35 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C B 35 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C B 35 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C B 35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C B 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C B 35 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 63 " -0.004 2.00e-02 2.50e+03 1.09e-02 3.54e+00 pdb=" N9 G B 63 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G B 63 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 63 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 63 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 63 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 63 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G B 63 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 63 " -0.028 2.00e-02 2.50e+03 pdb=" N2 G B 63 " 0.024 2.00e-02 2.50e+03 pdb=" N3 G B 63 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 63 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 53 " 0.022 2.00e-02 2.50e+03 1.04e-02 3.25e+00 pdb=" N9 G C 53 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G C 53 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G C 53 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 53 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 53 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 53 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G C 53 " 0.000 2.00e-02 2.50e+03 ... (remaining 616 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 640 2.67 - 3.23: 8176 3.23 - 3.79: 17008 3.79 - 4.34: 18215 4.34 - 4.90: 27169 Nonbonded interactions: 71208 Sorted by model distance: nonbonded pdb=" O4 U B 97 " pdb=" N6 A B 99 " model vdw 2.117 3.120 nonbonded pdb=" O4 U B 25 " pdb=" O6 G B 56 " model vdw 2.129 2.432 nonbonded pdb=" O2' G B 291 " pdb=" OP2 G B 293 " model vdw 2.139 3.040 nonbonded pdb=" O2' A B 248 " pdb=" O2' A C 74 " model vdw 2.186 3.040 nonbonded pdb=" O2' U B 366 " pdb=" O5' C B 367 " model vdw 2.207 3.040 ... (remaining 71203 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: 4.510 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11874 Z= 0.182 Angle : 2.227 77.348 18319 Z= 0.847 Chirality : 0.111 0.901 2412 Planarity : 0.004 0.029 619 Dihedral : 24.661 179.431 5826 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.04 % Allowed : 7.14 % Favored : 90.82 % 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: -0.20 (0.84), residues: 110 helix: 1.29 (0.81), residues: 45 sheet: -0.19 (1.14), residues: 12 loop : -1.41 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 PHE 0.011 0.002 PHE A 72 TRP 0.001 0.000 TRP A 108 HIS 0.004 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.18 (11874) covalent geometry : angle 2.22696 / 0.85 (18319) hydrogen bonds : bond 0.08457 / 4.90 ( 346) hydrogen bonds : angle 3.13363 / 2.23 ( 691) *********************** 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 **************************** Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6386 (mmt) cc_final: 0.5760 (tpp) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.1037 time to fit residues: 3.1657 Evaluate side-chains 10 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.4876 r_free = 0.4876 target = 0.146160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.127534 restraints weight = 89240.924| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.86 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 1.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.146 11874 Z= 0.549 Angle : 1.598 13.676 18319 Z= 0.754 Chirality : 0.070 0.434 2412 Planarity : 0.013 0.204 619 Dihedral : 26.846 177.967 5581 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 9.18 % Allowed : 11.22 % 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: -2.00 (0.75), residues: 110 helix: -1.12 (0.71), residues: 40 sheet: -1.06 (0.97), residues: 29 loop : -1.49 (0.94), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 73 PHE 0.024 0.006 PHE A 21 TRP 0.008 0.003 TRP A 108 HIS 0.017 0.008 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.55 (11874) covalent geometry : angle 1.59754 / 0.75 (18319) hydrogen bonds : bond 0.19361 / 12.04 ( 346) hydrogen bonds : angle 5.66698 / 3.86 ( 691) *********************** 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 **************************** Evaluate side-chains 28 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 27 average time/residue: 0.1622 time to fit residues: 5.4635 Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.129873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.119095 restraints weight = 95419.522| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.80 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 1.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11874 Z= 0.331 Angle : 1.129 9.762 18319 Z= 0.542 Chirality : 0.051 0.250 2412 Planarity : 0.008 0.061 619 Dihedral : 26.786 177.722 5581 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.10 % Allowed : 17.35 % 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: -3.05 (0.70), residues: 110 helix: -1.70 (0.63), residues: 41 sheet: -2.25 (0.84), residues: 31 loop : -1.79 (0.98), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 73 PHE 0.055 0.009 PHE A 19 TRP 0.001 0.001 TRP A 108 HIS 0.017 0.005 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.33 (11874) covalent geometry : angle 1.12943 / 0.54 (18319) hydrogen bonds : bond 0.12012 / 7.27 ( 346) hydrogen bonds : angle 3.96444 / 2.78 ( 691) *********************** 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 **************************** Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.109 Fit side-chains REVERT: A 82 MET cc_start: 0.6832 (tpp) cc_final: 0.6575 (tpp) REVERT: A 102 GLU cc_start: 0.8048 (pp20) cc_final: 0.6772 (tm-30) REVERT: A 105 GLU cc_start: 0.8090 (tp30) cc_final: 0.7790 (tp30) REVERT: A 106 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8128 (mtmm) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.1145 time to fit residues: 3.3681 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 101 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 0.0070 chunk 55 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 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 = 0.4501 r_free = 0.4501 target = 0.122216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.110506 restraints weight = 95869.848| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.37 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 1.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 11874 Z= 0.416 Angle : 1.265 12.159 18319 Z= 0.609 Chirality : 0.057 0.277 2412 Planarity : 0.009 0.076 619 Dihedral : 27.299 178.648 5581 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 6.12 % Allowed : 21.43 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.70), residues: 110 helix: -1.38 (0.68), residues: 40 sheet: -2.26 (0.87), residues: 31 loop : -2.53 (0.90), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 56 PHE 0.026 0.005 PHE A 19 TRP 0.002 0.001 TRP A 108 HIS 0.007 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.42 (11874) covalent geometry : angle 1.26548 / 0.61 (18319) hydrogen bonds : bond 0.14668 / 9.53 ( 346) hydrogen bonds : angle 4.73849 / 3.37 ( 691) *********************** 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 **************************** Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.184 Fit side-chains REVERT: A 102 GLU cc_start: 0.8378 (pp20) cc_final: 0.7376 (tm-30) REVERT: A 106 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8037 (mtmm) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.1329 time to fit residues: 3.7868 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.122862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.110902 restraints weight = 92800.023| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 1.79 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 1.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11874 Z= 0.263 Angle : 0.956 11.229 18319 Z= 0.459 Chirality : 0.045 0.290 2412 Planarity : 0.006 0.050 619 Dihedral : 26.908 179.106 5581 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 7.14 % Allowed : 22.45 % Favored : 70.41 % 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: -2.72 (0.71), residues: 110 helix: -0.81 (0.66), residues: 41 sheet: -2.31 (0.82), residues: 31 loop : -2.19 (0.96), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 57 PHE 0.023 0.004 PHE A 72 TRP 0.006 0.001 TRP A 108 HIS 0.011 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.26 (11874) covalent geometry : angle 0.95585 / 0.46 (18319) hydrogen bonds : bond 0.10628 / 6.47 ( 346) hydrogen bonds : angle 3.68752 / 2.64 ( 691) *********************** 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 **************************** Evaluate side-chains 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.145 Fit side-chains REVERT: A 102 GLU cc_start: 0.8389 (pp20) cc_final: 0.7415 (tm-30) REVERT: A 105 GLU cc_start: 0.8412 (tp30) cc_final: 0.8140 (tp30) REVERT: A 106 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8064 (mtmm) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.1029 time to fit residues: 3.4911 Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.117957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.105718 restraints weight = 91727.894| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.73 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 2.0117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11874 Z= 0.351 Angle : 1.131 12.213 18319 Z= 0.544 Chirality : 0.051 0.327 2412 Planarity : 0.008 0.072 619 Dihedral : 27.485 179.552 5581 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 7.14 % Allowed : 24.49 % Favored : 68.37 % 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: -2.92 (0.68), residues: 110 helix: -0.77 (0.66), residues: 39 sheet: -2.73 (0.87), residues: 23 loop : -2.44 (0.83), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 73 PHE 0.019 0.004 PHE A 19 TRP 0.003 0.001 TRP A 108 HIS 0.011 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.35 (11874) covalent geometry : angle 1.13063 / 0.54 (18319) hydrogen bonds : bond 0.12499 / 8.15 ( 346) hydrogen bonds : angle 4.44799 / 3.16 ( 691) *********************** 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 **************************** Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8393 (tp30) cc_final: 0.8090 (tp30) outliers start: 7 outliers final: 4 residues processed: 21 average time/residue: 0.1003 time to fit residues: 2.9924 Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.112425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.100028 restraints weight = 94492.016| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.96 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 2.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.102 11874 Z= 0.526 Angle : 1.430 13.721 18319 Z= 0.671 Chirality : 0.064 0.409 2412 Planarity : 0.009 0.072 619 Dihedral : 28.450 177.199 5581 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 42.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 8.16 % Allowed : 22.45 % Favored : 69.39 % 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: -4.51 (0.64), residues: 110 helix: -2.65 (0.59), residues: 41 sheet: -2.97 (0.73), residues: 31 loop : -3.00 (0.90), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 56 PHE 0.027 0.005 PHE A 19 TRP 0.009 0.003 TRP A 108 HIS 0.013 0.004 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00993 / 0.53 (11874) covalent geometry : angle 1.43029 / 0.67 (18319) hydrogen bonds : bond 0.17567 / 11.36 ( 346) hydrogen bonds : angle 5.30702 / 3.76 ( 691) *********************** 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 **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 22 average time/residue: 0.0891 time to fit residues: 2.7652 Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.117627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.105263 restraints weight = 90868.946| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.36 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 2.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11874 Z= 0.197 Angle : 0.863 9.653 18319 Z= 0.410 Chirality : 0.041 0.244 2412 Planarity : 0.005 0.032 619 Dihedral : 26.974 176.742 5581 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.08 % Allowed : 25.51 % Favored : 70.41 % 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: -3.07 (0.70), residues: 110 helix: -1.47 (0.65), residues: 42 sheet: -2.68 (0.73), residues: 30 loop : -1.74 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 PHE 0.012 0.003 PHE A 19 TRP 0.009 0.002 TRP A 108 HIS 0.005 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (11874) covalent geometry : angle 0.86262 / 0.41 (18319) hydrogen bonds : bond 0.08533 / 5.44 ( 346) hydrogen bonds : angle 3.78835 / 2.72 ( 691) *********************** 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 **************************** Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.110 Fit side-chains REVERT: A 106 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8919 (ptpp) outliers start: 4 outliers final: 2 residues processed: 18 average time/residue: 0.1088 time to fit residues: 2.8196 Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.113149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.100547 restraints weight = 93763.351| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.31 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 2.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 11874 Z= 0.393 Angle : 1.139 13.290 18319 Z= 0.540 Chirality : 0.052 0.288 2412 Planarity : 0.010 0.172 619 Dihedral : 27.618 178.441 5581 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.08 % Allowed : 27.55 % Favored : 68.37 % 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: -3.27 (0.74), residues: 110 helix: -1.46 (0.69), residues: 42 sheet: -2.91 (0.71), residues: 31 loop : -1.91 (1.13), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 110 PHE 0.015 0.004 PHE A 19 TRP 0.006 0.002 TRP A 108 HIS 0.016 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.39 (11874) covalent geometry : angle 1.13947 / 0.54 (18319) hydrogen bonds : bond 0.13145 / 8.58 ( 346) hydrogen bonds : angle 4.42223 / 3.12 ( 691) *********************** 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 **************************** Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.149 Fit side-chains REVERT: A 102 GLU cc_start: 0.8519 (pp20) cc_final: 0.8154 (pp20) REVERT: A 106 LYS cc_start: 0.9253 (mtmm) cc_final: 0.9004 (mtmm) outliers start: 4 outliers final: 4 residues processed: 17 average time/residue: 0.1055 time to fit residues: 2.6724 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.113965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.101312 restraints weight = 92618.323| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.76 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 2.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11874 Z= 0.292 Angle : 0.964 10.254 18319 Z= 0.459 Chirality : 0.045 0.238 2412 Planarity : 0.007 0.088 619 Dihedral : 27.145 179.177 5581 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.04 % Allowed : 31.63 % Favored : 66.33 % 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: -3.22 (0.72), residues: 110 helix: -1.50 (0.69), residues: 42 sheet: -3.32 (0.76), residues: 23 loop : -1.85 (0.96), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 56 PHE 0.016 0.003 PHE A 19 TRP 0.012 0.003 TRP A 108 HIS 0.011 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.29 (11874) covalent geometry : angle 0.96431 / 0.46 (18319) hydrogen bonds : bond 0.11166 / 6.98 ( 346) hydrogen bonds : angle 4.01961 / 2.86 ( 691) ********************** 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 **************************** Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.140 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0904 time to fit residues: 2.1094 Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.111440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.098841 restraints weight = 96128.543| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.43 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 2.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 11874 Z= 0.440 Angle : 1.201 11.218 18319 Z= 0.568 Chirality : 0.055 0.333 2412 Planarity : 0.008 0.077 619 Dihedral : 27.805 179.708 5581 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 32.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 6.12 % Allowed : 26.53 % Favored : 67.35 % 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: -3.60 (0.72), residues: 110 helix: -1.91 (0.66), residues: 40 sheet: -2.82 (0.75), residues: 31 loop : -2.15 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 98 PHE 0.015 0.004 PHE A 19 TRP 0.014 0.004 TRP A 108 HIS 0.018 0.004 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.44 (11874) covalent geometry : angle 1.20106 / 0.57 (18319) hydrogen bonds : bond 0.14445 / 9.33 ( 346) hydrogen bonds : angle 4.64606 / 3.27 ( 691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2540.12 seconds wall clock time: 44 minutes 13.17 seconds (2653.17 seconds total)