Starting phenix.real_space_refine on Wed Aug 5 22:16:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owt_70943/08_2026/9owt_70943.map" } resolution = 2.82 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= 0.007 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 29 9.91 5 P 515 5.49 5 S 3 5.16 5 C 5530 2.51 5 N 2189 2.21 5 O 3749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12015 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 14, 'rna3p_pur': 220, 'rna3p_pyr': 160} Link IDs: {'rna2p': 37, 'rna3p': 379} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1889 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 74} Chain: "E" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Unusual residues: {' CA': 28} Classifications: {'undetermined': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 12015 At special positions: 0 Unit cell: (128.563, 146.189, 172.109, 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 29 19.99 S 3 16.00 P 515 15.00 O 3749 8.00 N 2189 7.00 C 5530 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: 0.98 Conformation dependent library (CDL) restraints added in 175.9 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 48.3% alpha, 16.4% beta 174 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.708A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.090A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 440 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1148 1.33 - 1.44: 6363 1.44 - 1.56: 4773 1.56 - 1.68: 1026 1.68 - 1.80: 5 Bond restraints: 13315 Sorted by residual: bond pdb=" P A A 50 " pdb=" O5' A A 50 " ideal model delta sigma weight residual 1.593 1.551 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.13e+01 bond pdb=" N LEU B 111 " pdb=" CA LEU B 111 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.32e+00 bond pdb=" P C A 123 " pdb=" O5' C A 123 " ideal model delta sigma weight residual 1.593 1.622 -0.029 1.00e-02 1.00e+04 8.29e+00 bond pdb=" N VAL B 97 " pdb=" CA VAL B 97 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.62e+00 ... (remaining 13310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18438 2.33 - 4.66: 1449 4.66 - 7.00: 606 7.00 - 9.33: 47 9.33 - 11.66: 6 Bond angle restraints: 20546 Sorted by residual: angle pdb=" C3' C C 69 " pdb=" C2' C C 69 " pdb=" C1' C C 69 " ideal model delta sigma weight residual 101.30 96.93 4.37 7.00e-01 2.04e+00 3.89e+01 angle pdb=" C3' U A 52 " pdb=" O3' U A 52 " pdb=" P C A 53 " ideal model delta sigma weight residual 119.70 127.04 -7.34 1.20e+00 6.94e-01 3.74e+01 angle pdb=" C4' G A 236 " pdb=" C3' G A 236 " pdb=" C2' G A 236 " ideal model delta sigma weight residual 102.60 96.78 5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" C4' C C 69 " pdb=" C3' C C 69 " pdb=" C2' C C 69 " ideal model delta sigma weight residual 102.60 96.92 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" C4' A A 240 " pdb=" C3' A A 240 " pdb=" C2' A A 240 " ideal model delta sigma weight residual 102.60 97.47 5.13 1.00e+00 1.00e+00 2.63e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7065 35.94 - 71.88: 1423 71.88 - 107.82: 174 107.82 - 143.76: 6 143.76 - 179.70: 8 Dihedral angle restraints: 8676 sinusoidal: 8339 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 16.23 -176.23 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U C 59 " pdb=" C1' U C 59 " pdb=" N1 U C 59 " pdb=" C2 U C 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.34 179.66 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 232.00 58.55 173.45 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1859 0.112 - 0.224: 523 0.224 - 0.336: 61 0.336 - 0.448: 187 0.448 - 0.560: 81 Chirality restraints: 2711 Sorted by residual: chirality pdb=" P A C 75 " pdb=" OP1 A C 75 " pdb=" OP2 A C 75 " pdb=" O5' A C 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" P G E -13 " pdb=" OP1 G E -13 " pdb=" OP2 G E -13 " pdb=" O5' G E -13 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.59e+00 ... (remaining 2708 not shown) Planarity restraints: 679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.414 9.50e-02 1.11e+02 1.86e-01 2.11e+01 pdb=" NE ARG B 59 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 299 " 0.050 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G A 299 " -0.042 2.00e-02 2.50e+03 pdb=" C8 G A 299 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G A 299 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 299 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 299 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G A 299 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 299 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G A 299 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 299 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G A 299 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G A 299 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 187 " 0.038 2.00e-02 2.50e+03 1.64e-02 7.42e+00 pdb=" N9 A A 187 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A A 187 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A A 187 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A A 187 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 187 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A 187 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A A 187 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A A 187 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A 187 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A A 187 " -0.006 2.00e-02 2.50e+03 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 4 1.81 - 2.58: 171 2.58 - 3.36: 14360 3.36 - 4.13: 46478 4.13 - 4.90: 56847 Nonbonded interactions: 117860 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 523 " model vdw 1.038 2.510 nonbonded pdb=" OP2 A A 364 " pdb=" C8 G A 365 " model vdw 1.337 3.260 nonbonded pdb=" O3' A A 363 " pdb=" C8 A A 364 " model vdw 1.361 3.260 nonbonded pdb=" C3' A A 363 " pdb=" C8 A A 364 " model vdw 1.368 3.690 nonbonded pdb=" OP2 A A 364 " pdb=" N9 G A 365 " model vdw 1.835 3.120 ... (remaining 117855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.230 Find NCS groups from input model: 0.050 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.009 0.044 13315 Z= 0.683 Angle : 1.525 11.659 20546 Z= 0.921 Chirality : 0.160 0.560 2711 Planarity : 0.008 0.186 679 Dihedral : 27.542 179.700 8460 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 26.26 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.81), residues: 114 helix: 1.98 (0.83), residues: 46 sheet: 0.87 (0.82), residues: 29 loop : -0.02 (1.09), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 94 PHE 0.004 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.68 (13315) covalent geometry : angle 1.52466 / 0.92 (20546) hydrogen bonds : bond 0.18189 / 20.42 ( 487) hydrogen bonds : angle 8.99017 / 11.28 ( 875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8179 (mp0) REVERT: B 46 SER cc_start: 0.9299 (m) cc_final: 0.8974 (p) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.6891 time to fit residues: 17.9331 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.9990 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.085267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.051206 restraints weight = 47686.073| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.44 r_work: 0.2965 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 13315 Z= 0.545 Angle : 1.000 13.125 20546 Z= 0.503 Chirality : 0.071 0.606 2711 Planarity : 0.008 0.037 679 Dihedral : 26.760 175.193 8207 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.11 % Allowed : 23.23 % Favored : 65.66 % 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: 0.86 (0.81), residues: 114 helix: 1.27 (0.77), residues: 52 sheet: 0.38 (0.82), residues: 29 loop : -0.20 (1.22), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.012 0.003 TYR B 94 PHE 0.012 0.003 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.55 (13315) covalent geometry : angle 1.00028 / 0.50 (20546) hydrogen bonds : bond 0.12863 / 14.29 ( 487) hydrogen bonds : angle 2.86184 / 3.44 ( 875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8226 (mp0) REVERT: B 12 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: B 46 SER cc_start: 0.9441 (m) cc_final: 0.8980 (p) REVERT: B 92 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8837 (mtp) outliers start: 11 outliers final: 4 residues processed: 27 average time/residue: 0.7210 time to fit residues: 20.9112 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 50.0000 chunk 37 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 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 = 0.4110 r_free = 0.4110 target = 0.085883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.051892 restraints weight = 47843.254| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.80 r_work: 0.2967 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13315 Z= 0.337 Angle : 0.704 9.421 20546 Z= 0.385 Chirality : 0.049 0.475 2711 Planarity : 0.006 0.032 679 Dihedral : 26.614 179.431 8207 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 8.08 % Allowed : 26.26 % Favored : 65.66 % 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: 0.87 (0.81), residues: 114 helix: 1.90 (0.79), residues: 47 sheet: -0.05 (0.76), residues: 29 loop : -0.49 (1.19), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.008 0.002 TYR B 5 PHE 0.013 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.34 (13315) covalent geometry : angle 0.70351 / 0.38 (20546) hydrogen bonds : bond 0.09949 / 11.24 ( 487) hydrogen bonds : angle 2.66515 / 3.28 ( 875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8216 (mp0) REVERT: B 12 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: B 46 SER cc_start: 0.9413 (m) cc_final: 0.8940 (p) REVERT: B 92 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8844 (mtp) outliers start: 8 outliers final: 5 residues processed: 26 average time/residue: 0.7807 time to fit residues: 21.8743 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.085581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.051540 restraints weight = 47865.891| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 0.98 r_work: 0.2961 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13315 Z= 0.345 Angle : 0.735 11.241 20546 Z= 0.392 Chirality : 0.052 0.512 2711 Planarity : 0.006 0.033 679 Dihedral : 26.371 179.843 8207 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.06 % Allowed : 26.26 % Favored : 67.68 % 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: 0.58 (0.82), residues: 114 helix: 1.47 (0.75), residues: 47 sheet: -0.10 (0.79), residues: 29 loop : -0.46 (1.25), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 59 TYR 0.008 0.002 TYR B 40 PHE 0.010 0.002 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.34 (13315) covalent geometry : angle 0.73463 / 0.39 (20546) hydrogen bonds : bond 0.09800 / 10.81 ( 487) hydrogen bonds : angle 2.57644 / 3.14 ( 875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8168 (pm20) REVERT: B 12 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8673 (mt-10) REVERT: B 46 SER cc_start: 0.9415 (m) cc_final: 0.8938 (p) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.7683 time to fit residues: 20.6301 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 overall best weight: 4.0984 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.085273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051645 restraints weight = 47551.534| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.03 r_work: 0.2983 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13315 Z= 0.381 Angle : 0.754 11.152 20546 Z= 0.399 Chirality : 0.053 0.534 2711 Planarity : 0.006 0.032 679 Dihedral : 26.388 178.444 8207 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 8.08 % Allowed : 24.24 % Favored : 67.68 % 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: 0.50 (0.82), residues: 114 helix: 1.62 (0.79), residues: 46 sheet: -0.61 (0.79), residues: 31 loop : -0.30 (1.19), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.007 0.002 TYR B 31 PHE 0.013 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.38 (13315) covalent geometry : angle 0.75362 / 0.40 (20546) hydrogen bonds : bond 0.10006 / 11.14 ( 487) hydrogen bonds : angle 2.56931 / 3.18 ( 875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: B 12 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: B 46 SER cc_start: 0.9411 (m) cc_final: 0.8956 (p) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.8238 time to fit residues: 21.2024 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.085161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.051059 restraints weight = 47610.248| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.11 r_work: 0.2973 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13315 Z= 0.377 Angle : 0.737 9.446 20546 Z= 0.391 Chirality : 0.053 0.527 2711 Planarity : 0.006 0.031 679 Dihedral : 26.340 178.788 8207 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % 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: 0.48 (0.81), residues: 114 helix: 1.44 (0.76), residues: 47 sheet: -0.17 (0.80), residues: 29 loop : -0.59 (1.22), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.009 0.002 TYR B 5 PHE 0.012 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.38 (13315) covalent geometry : angle 0.73666 / 0.39 (20546) hydrogen bonds : bond 0.09850 / 10.84 ( 487) hydrogen bonds : angle 2.51510 / 3.10 ( 875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8043 (pm20) REVERT: B 12 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: B 46 SER cc_start: 0.9419 (m) cc_final: 0.8914 (p) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.7586 time to fit residues: 19.5834 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 50 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 2.9344 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.086656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051888 restraints weight = 48413.186| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 0.73 r_work: 0.2981 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13315 Z= 0.275 Angle : 0.618 8.314 20546 Z= 0.344 Chirality : 0.044 0.458 2711 Planarity : 0.005 0.027 679 Dihedral : 26.314 176.001 8207 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % Favored : 66.67 % 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: 0.55 (0.84), residues: 114 helix: 1.64 (0.79), residues: 47 sheet: -0.66 (0.81), residues: 31 loop : -0.20 (1.28), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.006 0.001 TYR B 31 PHE 0.010 0.002 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.28 (13315) covalent geometry : angle 0.61796 / 0.34 (20546) hydrogen bonds : bond 0.08563 / 9.45 ( 487) hydrogen bonds : angle 2.42219 / 3.00 ( 875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8024 (pm20) REVERT: B 12 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: B 46 SER cc_start: 0.9380 (m) cc_final: 0.8864 (p) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.7181 time to fit residues: 16.8683 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 50.0000 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.084607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.050565 restraints weight = 47298.731| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.40 r_work: 0.2945 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13315 Z= 0.530 Angle : 0.912 9.271 20546 Z= 0.459 Chirality : 0.066 0.636 2711 Planarity : 0.007 0.039 679 Dihedral : 26.339 179.373 8207 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 7.07 % Allowed : 28.28 % Favored : 64.65 % 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: 0.29 (0.80), residues: 114 helix: 1.20 (0.75), residues: 46 sheet: -0.08 (0.84), residues: 29 loop : -0.68 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.007 0.002 TYR B 5 PHE 0.012 0.003 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.53 (13315) covalent geometry : angle 0.91211 / 0.46 (20546) hydrogen bonds : bond 0.11796 / 12.89 ( 487) hydrogen bonds : angle 2.63646 / 3.26 ( 875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: B 12 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: B 46 SER cc_start: 0.9385 (m) cc_final: 0.8887 (p) outliers start: 7 outliers final: 2 residues processed: 23 average time/residue: 0.7642 time to fit residues: 18.8729 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.086559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051905 restraints weight = 48164.415| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 0.69 r_work: 0.2986 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13315 Z= 0.297 Angle : 0.651 7.907 20546 Z= 0.358 Chirality : 0.047 0.473 2711 Planarity : 0.005 0.024 679 Dihedral : 26.344 175.681 8207 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.03 % Allowed : 32.32 % Favored : 64.65 % 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: 0.50 (0.82), residues: 114 helix: 1.60 (0.78), residues: 47 sheet: -0.63 (0.81), residues: 31 loop : -0.30 (1.23), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.006 0.001 TYR B 31 PHE 0.011 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.30 (13315) covalent geometry : angle 0.65142 / 0.36 (20546) hydrogen bonds : bond 0.08833 / 9.68 ( 487) hydrogen bonds : angle 2.42921 / 3.01 ( 875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8089 (pm20) REVERT: B 12 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 46 SER cc_start: 0.9332 (m) cc_final: 0.8814 (p) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.8201 time to fit residues: 18.3735 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.086260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.051388 restraints weight = 48330.502| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 0.82 r_work: 0.2973 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13315 Z= 0.324 Angle : 0.687 8.011 20546 Z= 0.371 Chirality : 0.049 0.519 2711 Planarity : 0.006 0.031 679 Dihedral : 26.263 176.565 8207 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % Favored : 64.65 % 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: 0.51 (0.82), residues: 114 helix: 1.51 (0.79), residues: 46 sheet: -0.12 (0.81), residues: 29 loop : -0.60 (1.18), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.006 0.001 TYR B 94 PHE 0.012 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.32 (13315) covalent geometry : angle 0.68731 / 0.37 (20546) hydrogen bonds : bond 0.09424 / 10.23 ( 487) hydrogen bonds : angle 2.46401 / 3.06 ( 875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8000 (pm20) REVERT: B 12 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 46 SER cc_start: 0.9398 (m) cc_final: 0.8845 (p) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.7602 time to fit residues: 17.0608 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.085724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051054 restraints weight = 48603.532| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.27 r_work: 0.2948 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13315 Z= 0.440 Angle : 0.821 8.550 20546 Z= 0.426 Chirality : 0.059 0.599 2711 Planarity : 0.006 0.035 679 Dihedral : 26.294 178.312 8207 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.05 % Allowed : 30.30 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.81), residues: 114 helix: 1.37 (0.77), residues: 46 sheet: -0.04 (0.85), residues: 29 loop : -0.79 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 62 TYR 0.009 0.002 TYR B 5 PHE 0.012 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.44 (13315) covalent geometry : angle 0.82060 / 0.43 (20546) hydrogen bonds : bond 0.10873 / 11.82 ( 487) hydrogen bonds : angle 2.57490 / 3.20 ( 875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6322.99 seconds wall clock time: 108 minutes 6.40 seconds (6486.40 seconds total)