Starting phenix.real_space_refine on Wed Mar 4 04:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uo0_26636/03_2026/7uo0_26636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo0_26636/03_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_26636/03_2026/7uo0_26636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo0_26636/03_2026/7uo0_26636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo0_26636/03_2026/7uo0_26636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo0_26636/03_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-5986/lib/python3.9/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 dihedrals: 1 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: 2.30, per 1000 atoms: 0.22 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: 0.67 Conformation dependent library (CDL) restraints added in 224.8 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: 1.18 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: 1.66 Time building geometry restraints manager: 0.98 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: 6290 35.89 - 71.77: 1215 71.77 - 107.66: 181 107.66 - 143.55: 28 143.55 - 179.43: 31 Dihedral angle restraints: 7745 sinusoidal: 7420 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 7742 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.180 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3191 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 : 29.933 179.431 7531 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 covalent geometry : bond 0.00302 (11874) covalent geometry : angle 2.22696 (18319) hydrogen bonds : bond 0.08457 ( 346) hydrogen bonds : angle 3.13363 ( 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 : 0.105 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: 0.1347 time to fit residues: 3.9843 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 : 0.145 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 8.9990 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: 4.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.144436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.125138 restraints weight = 89618.099| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 4.70 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 1.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 11874 Z= 0.546 Angle : 1.668 13.090 18319 Z= 0.789 Chirality : 0.074 0.453 2412 Planarity : 0.014 0.224 619 Dihedral : 31.262 176.589 7286 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 34.55 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % Rotamer: Outliers : 8.16 % Allowed : 13.27 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.74), residues: 110 helix: -1.36 (0.70), residues: 40 sheet: -1.41 (0.93), residues: 30 loop : -1.34 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 110 PHE 0.026 0.006 PHE A 21 TRP 0.007 0.002 TRP A 108 HIS 0.014 0.006 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00992 (11874) covalent geometry : angle 1.66753 (18319) hydrogen bonds : bond 0.20992 ( 346) hydrogen bonds : angle 6.04029 ( 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: 8 poor density : 20 time to evaluate : 0.136 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 0.1842 time to fit residues: 6.2531 Evaluate side-chains 16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 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: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.117821 restraints weight = 93701.212| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.80 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 moved from start: 1.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11874 Z= 0.343 Angle : 1.184 10.438 18319 Z= 0.567 Chirality : 0.053 0.255 2412 Planarity : 0.008 0.073 619 Dihedral : 31.017 179.645 7286 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.10 % Allowed : 20.41 % Favored : 74.49 % 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 (0.68), residues: 110 helix: -1.55 (0.69), residues: 40 sheet: -2.45 (0.79), residues: 31 loop : -2.27 (0.86), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 98 PHE 0.069 0.008 PHE A 19 TRP 0.001 0.001 TRP A 108 HIS 0.006 0.003 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00639 (11874) covalent geometry : angle 1.18355 (18319) hydrogen bonds : bond 0.12704 ( 346) hydrogen bonds : angle 3.95662 ( 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 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.151 Fit side-chains REVERT: A 82 MET cc_start: 0.7018 (tpp) cc_final: 0.6734 (tpp) outliers start: 5 outliers final: 3 residues processed: 17 average time/residue: 0.1281 time to fit residues: 3.0451 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.118575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.106554 restraints weight = 91822.064| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.53 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 1.8077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 11874 Z= 0.467 Angle : 1.386 16.548 18319 Z= 0.665 Chirality : 0.062 0.303 2412 Planarity : 0.009 0.066 619 Dihedral : 31.536 175.498 7286 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 33.95 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: -3.39 (0.72), residues: 110 helix: -1.76 (0.74), residues: 39 sheet: -2.40 (0.84), residues: 31 loop : -2.31 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 98 PHE 0.053 0.006 PHE A 19 TRP 0.006 0.002 TRP A 108 HIS 0.007 0.003 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00886 (11874) covalent geometry : angle 1.38598 (18319) hydrogen bonds : bond 0.16062 ( 346) hydrogen bonds : angle 5.20373 ( 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 : 0.164 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8679 (tp30) cc_final: 0.8449 (tp30) outliers start: 6 outliers final: 3 residues processed: 20 average time/residue: 0.1327 time to fit residues: 3.6030 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.120217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.108221 restraints weight = 92037.666| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.99 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 1.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11874 Z= 0.323 Angle : 1.059 11.070 18319 Z= 0.509 Chirality : 0.049 0.268 2412 Planarity : 0.007 0.058 619 Dihedral : 31.244 177.983 7286 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 9.18 % Allowed : 23.47 % 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: -3.28 (0.72), residues: 110 helix: -1.47 (0.75), residues: 40 sheet: -2.54 (0.81), residues: 31 loop : -2.30 (0.93), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 57 PHE 0.074 0.006 PHE A 19 TRP 0.004 0.001 TRP A 108 HIS 0.005 0.002 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00606 (11874) covalent geometry : angle 1.05932 (18319) hydrogen bonds : bond 0.12104 ( 346) hydrogen bonds : angle 4.23893 ( 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 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.099 Fit side-chains REVERT: A 105 GLU cc_start: 0.8520 (tp30) cc_final: 0.8189 (tp30) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 0.1087 time to fit residues: 3.7839 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL 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: 6.9990 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: 0.6980 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.116457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.103826 restraints weight = 93508.568| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.94 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 2.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11874 Z= 0.356 Angle : 1.143 9.836 18319 Z= 0.546 Chirality : 0.052 0.270 2412 Planarity : 0.007 0.053 619 Dihedral : 31.396 178.845 7286 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 9.18 % Allowed : 25.51 % Favored : 65.31 % 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: -3.15 (0.74), residues: 110 helix: -1.62 (0.70), residues: 41 sheet: -3.03 (0.91), residues: 23 loop : -1.78 (0.94), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 57 PHE 0.029 0.004 PHE A 19 TRP 0.022 0.005 TRP A 108 HIS 0.007 0.002 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00662 (11874) covalent geometry : angle 1.14301 (18319) hydrogen bonds : bond 0.12776 ( 346) hydrogen bonds : angle 4.64322 ( 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 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.140 Fit side-chains REVERT: A 105 GLU cc_start: 0.8550 (tp30) cc_final: 0.8256 (tp30) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 0.1320 time to fit residues: 4.4909 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 : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 TRP 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: 10.0000 chunk 14 optimal weight: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.112341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.099886 restraints weight = 93905.248| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.43 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 2.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.094 11874 Z= 0.524 Angle : 1.396 13.668 18319 Z= 0.654 Chirality : 0.063 0.424 2412 Planarity : 0.009 0.077 619 Dihedral : 31.843 178.698 7286 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 41.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % 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: -4.42 (0.70), residues: 110 helix: -2.94 (0.62), residues: 41 sheet: -2.80 (0.76), residues: 31 loop : -2.61 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 73 PHE 0.079 0.008 PHE A 19 TRP 0.032 0.007 TRP A 108 HIS 0.010 0.003 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00985 (11874) covalent geometry : angle 1.39619 (18319) hydrogen bonds : bond 0.16849 ( 346) hydrogen bonds : angle 5.18458 ( 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 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.134 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 24 average time/residue: 0.1407 time to fit residues: 4.4800 Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.116144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.103645 restraints weight = 93055.655| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.83 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 2.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11874 Z= 0.224 Angle : 0.919 9.702 18319 Z= 0.435 Chirality : 0.043 0.254 2412 Planarity : 0.006 0.039 619 Dihedral : 31.096 177.011 7286 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.08 % Allowed : 29.59 % 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: -3.20 (0.75), residues: 110 helix: -1.58 (0.72), residues: 42 sheet: -2.68 (0.76), residues: 31 loop : -1.83 (1.11), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 73 PHE 0.055 0.004 PHE A 19 TRP 0.017 0.004 TRP A 108 HIS 0.007 0.002 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00412 (11874) covalent geometry : angle 0.91856 (18319) hydrogen bonds : bond 0.10407 ( 346) hydrogen bonds : angle 4.08252 ( 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: 4 poor density : 15 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8672 (tp30) cc_final: 0.8450 (tp30) outliers start: 4 outliers final: 1 residues processed: 16 average time/residue: 0.1395 time to fit residues: 3.0463 Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.112755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.099963 restraints weight = 92968.883| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.14 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 2.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11874 Z= 0.400 Angle : 1.162 13.127 18319 Z= 0.547 Chirality : 0.053 0.296 2412 Planarity : 0.007 0.048 619 Dihedral : 31.510 179.314 7286 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 31.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 3.06 % Allowed : 29.59 % 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: -3.34 (0.79), residues: 110 helix: -1.57 (0.77), residues: 42 sheet: -2.79 (0.77), residues: 31 loop : -2.05 (1.18), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 PHE 0.075 0.006 PHE A 19 TRP 0.024 0.005 TRP A 108 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00749 (11874) covalent geometry : angle 1.16158 (18319) hydrogen bonds : bond 0.14353 ( 346) hydrogen bonds : angle 4.58600 ( 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: 3 poor density : 16 time to evaluate : 0.096 Fit side-chains REVERT: A 105 GLU cc_start: 0.8681 (tp30) cc_final: 0.8436 (tp30) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.1304 time to fit residues: 2.9615 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL 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 14 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.113696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.101223 restraints weight = 92692.689| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.89 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 2.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11874 Z= 0.302 Angle : 0.968 10.494 18319 Z= 0.458 Chirality : 0.045 0.266 2412 Planarity : 0.007 0.098 619 Dihedral : 31.168 179.111 7286 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.06 % Allowed : 31.63 % Favored : 65.31 % 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: -3.18 (0.76), residues: 110 helix: -1.43 (0.75), residues: 42 sheet: -3.51 (0.67), residues: 23 loop : -1.73 (1.02), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 110 PHE 0.066 0.005 PHE A 19 TRP 0.016 0.003 TRP A 108 HIS 0.014 0.003 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00569 (11874) covalent geometry : angle 0.96846 (18319) hydrogen bonds : bond 0.11505 ( 346) hydrogen bonds : angle 4.10406 ( 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 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.136 Fit side-chains REVERT: A 105 GLU cc_start: 0.8765 (tp30) cc_final: 0.8512 (tp30) outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.1039 time to fit residues: 2.0585 Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 48 LEU 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: 3.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.111496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.099008 restraints weight = 96267.134| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.03 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 2.5201 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= 0.410 Angle : 1.153 12.968 18319 Z= 0.544 Chirality : 0.053 0.318 2412 Planarity : 0.008 0.060 619 Dihedral : 31.465 178.693 7286 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 2.04 % Allowed : 32.65 % Favored : 65.31 % 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: -3.31 (0.79), residues: 110 helix: -1.45 (0.77), residues: 41 sheet: -2.78 (0.77), residues: 31 loop : -2.17 (1.18), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 110 PHE 0.076 0.006 PHE A 19 TRP 0.028 0.006 TRP A 108 HIS 0.007 0.003 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00773 (11874) covalent geometry : angle 1.15338 (18319) hydrogen bonds : bond 0.14697 ( 346) hydrogen bonds : angle 4.61585 ( 691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2763.74 seconds wall clock time: 47 minutes 53.19 seconds (2873.19 seconds total)