Starting phenix.real_space_refine on Fri Sep 11 17:42:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo0_26636/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.map" model { file = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo0_26636/09_2026/7uo0_26636.cif" } 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-2.2.1-6174/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: {'RNAv2': 373} Modifications used: {'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: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1744 Classifications: {'RNAv2': 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: 2.03, per 1000 atoms: 0.19 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: 0.75 Conformation dependent library (CDL) restraints added in 67.4 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: 1.23 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: 1.41 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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=" O3' U C 34 " pdb=" P C C 35 " ideal model delta sigma weight residual 1.607 1.625 -0.018 1.20e-02 6.94e+03 2.29e+00 bond pdb=" C3' G C 19 " pdb=" O3' G C 19 " ideal model delta sigma weight residual 1.415 1.440 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C3' A B 192 " pdb=" O3' A B 192 " ideal model delta sigma weight residual 1.415 1.439 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C3' U C 34 " pdb=" O3' U C 34 " ideal model delta sigma weight residual 1.415 1.439 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C2 U B 34 " pdb=" O2 U B 34 " ideal model delta sigma weight residual 1.219 1.243 -0.024 2.00e-02 2.50e+03 1.39e+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 - 35.44: 5225 35.44 - 70.89: 708 70.89 - 106.33: 76 106.33 - 141.77: 7 141.77 - 177.22: 24 Dihedral angle restraints: 6040 sinusoidal: 5715 harmonic: 325 Sorted by residual: dihedral pdb=" C4' U B 191 " pdb=" C3' U B 191 " pdb=" C2' U B 191 " pdb=" C1' U B 191 " ideal model delta sinusoidal sigma weight residual 36.34 -37.07 73.42 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' G B 194 " pdb=" C3' G B 194 " pdb=" C2' G B 194 " pdb=" C1' G B 194 " ideal model delta sinusoidal sigma weight residual 36.35 -36.66 73.00 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G B 82 " pdb=" C3' G B 82 " pdb=" C2' G B 82 " pdb=" C1' G B 82 " ideal model delta sinusoidal sigma weight residual 36.34 -36.47 72.81 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1818 0.160 - 0.320: 306 0.320 - 0.481: 131 0.481 - 0.641: 144 0.641 - 0.801: 13 Chirality restraints: 2412 Sorted by residual: chirality pdb=" P A B 193 " pdb=" OP1 A B 193 " pdb=" OP2 A B 193 " pdb=" O5' A B 193 " both_signs ideal model delta sigma weight residual True 2.17 -2.97 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" P C C 35 " pdb=" OP1 C C 35 " pdb=" OP2 C C 35 " pdb=" O5' C C 35 " both_signs ideal model delta sigma weight residual True 2.17 -2.91 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" P G C 10 " pdb=" OP1 G C 10 " pdb=" OP2 G C 10 " pdb=" O5' G C 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.91 -0.74 2.00e-01 2.50e+01 1.36e+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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.870 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- 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 0.025 11874 Z= 0.161 Angle : 2.261 77.348 18319 Z= 0.785 Chirality : 0.195 0.801 2412 Planarity : 0.004 0.029 619 Dihedral : 24.820 177.218 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 0.00314 / 0.16 (11874) covalent geometry : angle 2.26096 / 0.79 (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 : 0.097 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: 0.1248 time to fit residues: 3.7753 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 : 0.139 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.153188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.133041 restraints weight = 88197.485| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 3.01 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 moved from start: 0.8460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 11874 Z= 0.479 Angle : 2.109 25.721 18319 Z= 0.804 Chirality : 0.129 1.970 2412 Planarity : 0.009 0.116 619 Dihedral : 24.549 173.849 5581 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.91 % Allowed : 5.45 % Favored : 93.64 % Rotamer: Outliers : 7.14 % Allowed : 15.31 % 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: -2.00 (0.78), residues: 110 helix: -1.38 (0.66), residues: 46 sheet: -0.99 (0.94), residues: 28 loop : -1.13 (1.19), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 45 PHE 0.029 0.005 PHE A 19 TRP 0.011 0.003 TRP A 108 HIS 0.025 0.008 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.48 (11874) covalent geometry : angle 2.10922 / 0.80 (18319) hydrogen bonds : bond 0.16107 / 9.64 ( 346) hydrogen bonds : angle 5.08904 / 3.50 ( 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 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.120 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 19 average time/residue: 0.1173 time to fit residues: 3.0113 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU 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: 0.7980 chunk 27 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4902 r_free = 0.4902 target = 0.146895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.127318 restraints weight = 86591.108| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.64 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 1.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 11874 Z= 0.339 Angle : 1.625 25.949 18319 Z= 0.625 Chirality : 0.114 1.913 2412 Planarity : 0.008 0.068 619 Dihedral : 24.813 177.126 5581 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 3.06 % Allowed : 21.43 % Favored : 75.51 % 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: -2.94 (0.76), residues: 110 helix: -1.87 (0.66), residues: 48 sheet: -1.68 (1.03), residues: 24 loop : -1.87 (1.06), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 98 PHE 0.054 0.007 PHE A 19 TRP 0.004 0.001 TRP A 108 HIS 0.017 0.005 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.34 (11874) covalent geometry : angle 1.62476 / 0.63 (18319) hydrogen bonds : bond 0.11352 / 6.77 ( 346) hydrogen bonds : angle 3.93088 / 2.83 ( 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 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.158 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 0.1860 time to fit residues: 5.4217 Evaluate side-chains 14 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** 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 = 0.4568 r_free = 0.4568 target = 0.125221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.113838 restraints weight = 96029.717| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.66 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 1.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 11874 Z= 0.405 Angle : 1.796 22.203 18319 Z= 0.689 Chirality : 0.121 2.010 2412 Planarity : 0.009 0.072 619 Dihedral : 24.960 176.530 5581 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.91 % Favored : 88.18 % 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: -3.84 (0.67), residues: 110 helix: -2.69 (0.60), residues: 40 sheet: -2.07 (0.81), residues: 31 loop : -2.45 (0.94), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 37 PHE 0.025 0.004 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.011 0.005 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.41 (11874) covalent geometry : angle 1.79625 / 0.69 (18319) hydrogen bonds : bond 0.14143 / 8.34 ( 346) hydrogen bonds : angle 4.82613 / 3.50 ( 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 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8400 (tp30) cc_final: 0.8192 (tp30) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.1183 time to fit residues: 3.6027 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 : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 59 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.123213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.111317 restraints weight = 94426.396| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 1.52 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 1.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11874 Z= 0.335 Angle : 1.614 25.651 18319 Z= 0.617 Chirality : 0.111 1.913 2412 Planarity : 0.008 0.065 619 Dihedral : 25.184 179.611 5581 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 7.14 % Allowed : 25.51 % 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: -3.88 (0.68), residues: 110 helix: -2.53 (0.60), residues: 45 sheet: -2.02 (0.88), residues: 29 loop : -2.69 (0.92), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 98 PHE 0.086 0.008 PHE A 19 TRP 0.003 0.001 TRP A 108 HIS 0.010 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.33 (11874) covalent geometry : angle 1.61443 / 0.62 (18319) hydrogen bonds : bond 0.11852 / 6.98 ( 346) hydrogen bonds : angle 4.18861 / 3.04 ( 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 26 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.144 Fit side-chains REVERT: A 105 GLU cc_start: 0.8420 (tp30) cc_final: 0.7683 (tp30) REVERT: A 109 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7818 (tpp-160) outliers start: 7 outliers final: 3 residues processed: 23 average time/residue: 0.1352 time to fit residues: 4.1835 Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 108 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.110924 restraints weight = 93099.537| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.43 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 1.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11874 Z= 0.265 Angle : 1.453 22.748 18319 Z= 0.553 Chirality : 0.103 1.926 2412 Planarity : 0.006 0.048 619 Dihedral : 24.976 178.303 5581 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 3.06 % Allowed : 34.69 % Favored : 62.24 % 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: -3.02 (0.69), residues: 110 helix: -1.66 (0.69), residues: 41 sheet: -1.74 (0.80), residues: 31 loop : -2.31 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 57 PHE 0.018 0.003 PHE A 19 TRP 0.002 0.001 TRP A 108 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.27 (11874) covalent geometry : angle 1.45265 / 0.55 (18319) hydrogen bonds : bond 0.10075 / 6.00 ( 346) hydrogen bonds : angle 4.09289 / 2.97 ( 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 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.110 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 21 average time/residue: 0.1139 time to fit residues: 3.2140 Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.115041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.102801 restraints weight = 95839.716| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.60 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 2.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 11874 Z= 0.483 Angle : 1.948 23.398 18319 Z= 0.744 Chirality : 0.128 1.880 2412 Planarity : 0.009 0.067 619 Dihedral : 25.787 178.921 5581 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 32.42 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.82 % Favored : 87.27 % Rotamer: Outliers : 8.16 % Allowed : 29.59 % Favored : 62.24 % 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: -3.65 (0.70), residues: 110 helix: -2.02 (0.72), residues: 39 sheet: -1.92 (0.81), residues: 31 loop : -3.01 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 61 PHE 0.024 0.005 PHE A 19 TRP 0.012 0.003 TRP A 108 HIS 0.009 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.48 (11874) covalent geometry : angle 1.94844 / 0.74 (18319) hydrogen bonds : bond 0.15238 / 9.85 ( 346) hydrogen bonds : angle 5.13483 / 3.66 ( 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 : 0.148 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 22 average time/residue: 0.1283 time to fit residues: 3.8119 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 59 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.119963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.108017 restraints weight = 90626.342| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 1.46 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 2.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11874 Z= 0.216 Angle : 1.388 24.712 18319 Z= 0.528 Chirality : 0.103 1.910 2412 Planarity : 0.006 0.032 619 Dihedral : 25.202 179.771 5581 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.02 % Allowed : 34.69 % Favored : 64.29 % 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: -3.02 (0.70), residues: 110 helix: -1.57 (0.74), residues: 41 sheet: -1.81 (0.77), residues: 29 loop : -2.35 (0.90), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 PHE 0.020 0.003 PHE A 19 TRP 0.010 0.003 TRP A 108 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (11874) covalent geometry : angle 1.38840 / 0.53 (18319) hydrogen bonds : bond 0.08834 / 5.45 ( 346) hydrogen bonds : angle 4.09341 / 2.96 ( 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 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.161 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1352 time to fit residues: 3.5552 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.103768 restraints weight = 92564.858| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.50 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 2.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11874 Z= 0.365 Angle : 1.642 23.972 18319 Z= 0.628 Chirality : 0.114 1.894 2412 Planarity : 0.007 0.039 619 Dihedral : 25.275 179.255 5581 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.04 % Allowed : 34.69 % Favored : 63.27 % 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: -3.42 (0.71), residues: 110 helix: -1.77 (0.72), residues: 42 sheet: -2.26 (0.73), residues: 31 loop : -2.52 (1.01), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 98 PHE 0.024 0.004 PHE A 17 TRP 0.012 0.003 TRP A 108 HIS 0.010 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.36 (11874) covalent geometry : angle 1.64205 / 0.63 (18319) hydrogen bonds : bond 0.12229 / 7.58 ( 346) hydrogen bonds : angle 4.50292 / 3.19 ( 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 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.144 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1524 time to fit residues: 4.2591 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.117413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.105458 restraints weight = 92220.989| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.38 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 2.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11874 Z= 0.270 Angle : 1.437 23.746 18319 Z= 0.549 Chirality : 0.104 1.878 2412 Planarity : 0.007 0.096 619 Dihedral : 25.159 179.877 5581 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.02 % Allowed : 34.69 % Favored : 64.29 % 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: -3.28 (0.69), residues: 110 helix: -1.77 (0.70), residues: 42 sheet: -2.21 (0.72), residues: 31 loop : -2.27 (0.97), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 110 PHE 0.016 0.003 PHE A 19 TRP 0.014 0.003 TRP A 108 HIS 0.007 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (11874) covalent geometry : angle 1.43652 / 0.55 (18319) hydrogen bonds : bond 0.09854 / 6.00 ( 346) hydrogen bonds : angle 4.17027 / 2.98 ( 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 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.161 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1430 time to fit residues: 3.5307 Evaluate side-chains 17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.114230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.102053 restraints weight = 93966.074| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.57 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 2.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11874 Z= 0.381 Angle : 1.680 23.779 18319 Z= 0.642 Chirality : 0.117 1.883 2412 Planarity : 0.007 0.047 619 Dihedral : 25.426 179.987 5581 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 1.02 % Allowed : 34.69 % Favored : 64.29 % 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: -3.66 (0.71), residues: 110 helix: -1.98 (0.71), residues: 42 sheet: -2.56 (0.70), residues: 31 loop : -2.44 (1.05), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 110 PHE 0.022 0.004 PHE A 17 TRP 0.013 0.003 TRP A 108 HIS 0.011 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.38 (11874) covalent geometry : angle 1.68041 / 0.64 (18319) hydrogen bonds : bond 0.12499 / 7.76 ( 346) hydrogen bonds : angle 4.61969 / 3.26 ( 691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.10 seconds wall clock time: 47 minutes 57.79 seconds (2877.79 seconds total)