Starting phenix.real_space_refine on Wed Aug 5 23:12:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owy_70948/08_2026/9owy_70948.map" } resolution = 2.69 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 525 5.49 5 S 3 5.16 5 C 5626 2.51 5 N 2231 2.21 5 O 3817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12231 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 26, 'rna2p_pyr': 15, 'rna3p_pur': 217, 'rna3p_pyr': 159} Link IDs: {'rna2p': 41, 'rna3p': 375} 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: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2293 Classifications: {'RNA': 108} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 41, 'rna3p_pyr': 50} Link IDs: {'rna2p': 16, 'rna3p': 91} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Unusual residues: {' CA': 27} Classifications: {'undetermined': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.48, per 1000 atoms: 0.20 Number of scatterers: 12231 At special positions: 0 Unit cell: (120.269, 159.667, 128.563, 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 525 15.00 O 3817 8.00 N 2231 7.00 C 5626 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: 0.90 Conformation dependent library (CDL) restraints added in 197.0 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: 4 helices and 1 sheets defined 44.0% alpha, 16.4% beta 184 base pairs and 308 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... 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: 3.526A 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: 6.191A 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: 7.236A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 467 hydrogen bonds 772 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 308 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1131 1.32 - 1.44: 6478 1.44 - 1.56: 4895 1.56 - 1.68: 1049 1.68 - 1.80: 5 Bond restraints: 13558 Sorted by residual: bond pdb=" CA SER B 100 " pdb=" CB SER B 100 " ideal model delta sigma weight residual 1.529 1.422 0.107 1.55e-02 4.16e+03 4.73e+01 bond pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.37e-02 5.33e+03 2.19e+01 bond pdb=" CA ALA B 95 " pdb=" CB ALA B 95 " ideal model delta sigma weight residual 1.532 1.460 0.072 1.65e-02 3.67e+03 1.88e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.20e+01 bond pdb=" P A A 50 " pdb=" O5' A A 50 " ideal model delta sigma weight residual 1.593 1.564 0.029 1.00e-02 1.00e+04 8.29e+00 ... (remaining 13553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18525 2.36 - 4.72: 1632 4.72 - 7.08: 716 7.08 - 9.45: 51 9.45 - 11.81: 4 Bond angle restraints: 20928 Sorted by residual: angle pdb=" C4' G C 44 " pdb=" O4' G C 44 " pdb=" C1' G C 44 " ideal model delta sigma weight residual 109.70 105.25 4.45 7.00e-01 2.04e+00 4.04e+01 angle pdb=" O4' A A 137 " pdb=" C4' A A 137 " pdb=" C3' A A 137 " ideal model delta sigma weight residual 106.10 101.34 4.76 8.00e-01 1.56e+00 3.55e+01 angle pdb=" O3' C A 92 " pdb=" P C A 93 " pdb=" O5' C A 93 " ideal model delta sigma weight residual 104.00 94.29 9.71 1.90e+00 2.77e-01 2.61e+01 angle pdb=" N LYS B 4 " pdb=" CA LYS B 4 " pdb=" C LYS B 4 " ideal model delta sigma weight residual 111.82 105.98 5.84 1.16e+00 7.43e-01 2.54e+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 97.62 4.98 1.00e+00 1.00e+00 2.48e+01 ... (remaining 20923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 7157 35.87 - 71.75: 1480 71.75 - 107.62: 185 107.62 - 143.50: 9 143.50 - 179.37: 8 Dihedral angle restraints: 8839 sinusoidal: 8502 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 9.40 -169.40 1 1.50e+01 4.44e-03 8.46e+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 -128.00 51.37 -179.37 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C C -4 " pdb=" C1' C C -4 " pdb=" N1 C C -4 " pdb=" C2 C C -4 " ideal model delta sinusoidal sigma weight residual 232.00 54.43 177.57 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1906 0.125 - 0.249: 476 0.249 - 0.374: 150 0.374 - 0.498: 213 0.498 - 0.623: 16 Chirality restraints: 2761 Sorted by residual: chirality pdb=" P G A 268 " pdb=" OP1 G A 268 " pdb=" OP2 G A 268 " pdb=" O5' G A 268 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" P C A 123 " pdb=" OP1 C A 123 " pdb=" OP2 C A 123 " pdb=" O5' C A 123 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" P G A 127 " pdb=" OP1 G A 127 " pdb=" OP2 G A 127 " pdb=" O5' G A 127 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.32e+00 ... (remaining 2758 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.412 9.50e-02 1.11e+02 1.85e-01 2.10e+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=" CA GLY B 110 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLY B 110 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY B 110 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 111 " 0.023 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 2.04e-02 1.25e+01 pdb=" N9 G A 299 " -0.042 2.00e-02 2.50e+03 pdb=" C8 G A 299 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G A 299 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 299 " 0.001 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 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 5 1.81 - 2.58: 213 2.58 - 3.35: 14572 3.35 - 4.13: 47795 4.13 - 4.90: 58483 Nonbonded interactions: 121068 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 521 " model vdw 1.037 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 C A 196 " pdb="CA CA A 525 " model vdw 1.770 2.510 ... (remaining 121063 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: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.020 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 0.107 13558 Z= 0.734 Angle : 1.625 11.808 20928 Z= 0.967 Chirality : 0.167 0.623 2761 Planarity : 0.009 0.185 689 Dihedral : 27.939 179.369 8623 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 1.75 % Allowed : 2.63 % Favored : 95.61 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % 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: 0.77 (0.79), residues: 114 helix: 1.16 (0.85), residues: 47 sheet: 0.87 (0.83), residues: 29 loop : -0.50 (0.96), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.006 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 0.00948 / 0.73 (13558) covalent geometry : angle 1.62511 / 0.97 (20928) hydrogen bonds : bond 0.21176 / 22.90 ( 512) hydrogen bonds : angle 10.09485 / 13.20 ( 901) *********************** 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 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.165 Fit side-chains REVERT: B 4 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9074 (tttp) REVERT: B 12 GLU cc_start: 0.8739 (mp0) cc_final: 0.8314 (mt-10) REVERT: B 112 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7151 (mppt) outliers start: 9 outliers final: 0 residues processed: 34 average time/residue: 0.7669 time to fit residues: 27.7387 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.099983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.059980 restraints weight = 40859.843| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.32 r_work: 0.3075 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 13558 Z= 0.550 Angle : 0.966 9.577 20928 Z= 0.501 Chirality : 0.068 0.374 2761 Planarity : 0.008 0.034 689 Dihedral : 26.983 179.253 8376 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.11 % Allowed : 18.18 % Favored : 70.71 % 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: 0.56 (0.76), residues: 114 helix: 0.55 (0.71), residues: 48 sheet: 0.72 (0.83), residues: 29 loop : 0.09 (1.14), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 86 TYR 0.013 0.003 TYR B 31 PHE 0.023 0.005 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00857 / 0.55 (13558) covalent geometry : angle 0.96595 / 0.50 (20928) hydrogen bonds : bond 0.13801 / 14.13 ( 512) hydrogen bonds : angle 3.08382 / 4.08 ( 901) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8403 (mp0) cc_final: 0.8190 (mp0) REVERT: B 12 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8740 (mt-10) REVERT: B 112 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7718 (mmtp) outliers start: 11 outliers final: 2 residues processed: 25 average time/residue: 0.8491 time to fit residues: 22.5994 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 : 0.164 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.099946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.060681 restraints weight = 41311.004| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.01 r_work: 0.3067 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 13558 Z= 0.445 Angle : 0.786 10.364 20928 Z= 0.423 Chirality : 0.053 0.372 2761 Planarity : 0.007 0.027 689 Dihedral : 26.756 175.621 8372 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 9.09 % Allowed : 18.18 % Favored : 72.73 % 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: 0.49 (0.76), residues: 114 helix: 0.66 (0.71), residues: 48 sheet: 0.06 (0.73), residues: 29 loop : 0.41 (1.21), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.010 0.002 TYR B 94 PHE 0.017 0.004 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.45 (13558) covalent geometry : angle 0.78641 / 0.42 (20928) hydrogen bonds : bond 0.11456 / 12.17 ( 512) hydrogen bonds : angle 2.87284 / 3.72 ( 901) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.165 Fit side-chains REVERT: B 12 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: B 86 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8815 (mtp85) outliers start: 9 outliers final: 3 residues processed: 26 average time/residue: 0.8663 time to fit residues: 23.9293 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.099786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060140 restraints weight = 40870.449| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.97 r_work: 0.3070 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 13558 Z= 0.400 Angle : 0.760 10.485 20928 Z= 0.408 Chirality : 0.054 0.373 2761 Planarity : 0.007 0.026 689 Dihedral : 26.573 176.477 8368 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 8.08 % Allowed : 21.21 % Favored : 70.71 % 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: 0.74 (0.79), residues: 114 helix: 0.68 (0.74), residues: 48 sheet: 0.54 (0.80), residues: 29 loop : 0.49 (1.23), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.018 0.003 TYR B 94 PHE 0.016 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.40 (13558) covalent geometry : angle 0.76005 / 0.41 (20928) hydrogen bonds : bond 0.10726 / 11.18 ( 512) hydrogen bonds : angle 2.63195 / 3.44 ( 901) *********************** 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: 8 poor density : 19 time to evaluate : 0.148 Fit side-chains REVERT: B 19 GLN cc_start: 0.9051 (mp10) cc_final: 0.8600 (mt0) outliers start: 8 outliers final: 3 residues processed: 23 average time/residue: 0.7861 time to fit residues: 19.2632 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.097648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.059135 restraints weight = 37776.334| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.36 r_work: 0.3104 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 13558 Z= 0.556 Angle : 0.891 9.004 20928 Z= 0.458 Chirality : 0.064 0.370 2761 Planarity : 0.007 0.032 689 Dihedral : 26.635 176.401 8368 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.06 % Allowed : 23.23 % Favored : 70.71 % 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: 0.05 (0.77), residues: 114 helix: 0.11 (0.69), residues: 48 sheet: 0.10 (0.82), residues: 29 loop : 0.22 (1.20), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.013 0.002 TYR B 94 PHE 0.020 0.004 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.56 (13558) covalent geometry : angle 0.89085 / 0.46 (20928) hydrogen bonds : bond 0.12545 / 13.26 ( 512) hydrogen bonds : angle 2.72643 / 3.51 ( 901) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.109 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 23 average time/residue: 0.8336 time to fit residues: 20.2998 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 50.0000 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.099212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.061144 restraints weight = 37600.343| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.74 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13558 Z= 0.284 Angle : 0.618 8.117 20928 Z= 0.352 Chirality : 0.043 0.364 2761 Planarity : 0.006 0.032 689 Dihedral : 26.579 175.242 8368 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 25.25 % 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: 0.55 (0.80), residues: 114 helix: 0.85 (0.77), residues: 47 sheet: 0.73 (0.84), residues: 26 loop : -0.30 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.015 0.002 TYR B 94 PHE 0.013 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.28 (13558) covalent geometry : angle 0.61771 / 0.35 (20928) hydrogen bonds : bond 0.09466 / 9.98 ( 512) hydrogen bonds : angle 2.46841 / 3.16 ( 901) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.168 Fit side-chains REVERT: B 19 GLN cc_start: 0.8996 (mp10) cc_final: 0.8536 (mt0) outliers start: 6 outliers final: 1 residues processed: 22 average time/residue: 0.7550 time to fit residues: 17.6793 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.098873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060775 restraints weight = 37521.634| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.76 r_work: 0.3140 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13558 Z= 0.283 Angle : 0.622 8.289 20928 Z= 0.349 Chirality : 0.044 0.361 2761 Planarity : 0.006 0.024 689 Dihedral : 26.386 176.145 8368 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 27.27 % 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: 0.44 (0.80), residues: 114 helix: 0.66 (0.77), residues: 48 sheet: 0.88 (0.84), residues: 26 loop : -0.41 (1.14), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG B 42 TYR 0.011 0.002 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.28 (13558) covalent geometry : angle 0.62218 / 0.35 (20928) hydrogen bonds : bond 0.09744 / 10.35 ( 512) hydrogen bonds : angle 2.48924 / 3.16 ( 901) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.162 Fit side-chains REVERT: B 19 GLN cc_start: 0.8979 (mp10) cc_final: 0.8542 (mt0) outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 0.7951 time to fit residues: 18.5927 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.099165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061163 restraints weight = 37449.447| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 0.74 r_work: 0.3154 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13558 Z= 0.256 Angle : 0.578 8.137 20928 Z= 0.333 Chirality : 0.041 0.361 2761 Planarity : 0.005 0.029 689 Dihedral : 26.388 175.519 8368 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.06 % Allowed : 25.25 % 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: 0.61 (0.83), residues: 114 helix: 0.82 (0.79), residues: 47 sheet: 0.94 (0.83), residues: 26 loop : -0.30 (1.18), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.015 0.002 TYR B 94 PHE 0.010 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.26 (13558) covalent geometry : angle 0.57832 / 0.33 (20928) hydrogen bonds : bond 0.09212 / 9.77 ( 512) hydrogen bonds : angle 2.43343 / 3.11 ( 901) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.171 Fit side-chains REVERT: B 19 GLN cc_start: 0.8999 (mp10) cc_final: 0.8520 (mt0) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 0.7703 time to fit residues: 18.9142 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 : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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 = 0.097122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058794 restraints weight = 37596.841| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.48 r_work: 0.3071 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 13558 Z= 0.631 Angle : 0.964 10.960 20928 Z= 0.485 Chirality : 0.070 0.371 2761 Planarity : 0.008 0.045 689 Dihedral : 26.492 176.846 8368 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.06 % Allowed : 25.25 % 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: -0.30 (0.77), residues: 114 helix: -0.05 (0.71), residues: 47 sheet: 0.54 (0.80), residues: 26 loop : -0.69 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.012 0.003 TYR B 94 PHE 0.019 0.005 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.63 (13558) covalent geometry : angle 0.96360 / 0.48 (20928) hydrogen bonds : bond 0.13168 / 13.91 ( 512) hydrogen bonds : angle 2.75570 / 3.48 ( 901) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.104 Fit side-chains REVERT: B 19 GLN cc_start: 0.9057 (mp10) cc_final: 0.8625 (mt0) outliers start: 6 outliers final: 2 residues processed: 20 average time/residue: 0.8092 time to fit residues: 17.2242 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.097827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059758 restraints weight = 37789.649| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.15 r_work: 0.3096 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 13558 Z= 0.486 Angle : 0.798 7.950 20928 Z= 0.422 Chirality : 0.057 0.371 2761 Planarity : 0.007 0.032 689 Dihedral : 26.589 176.258 8368 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.04 % Allowed : 28.28 % 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: -0.21 (0.77), residues: 114 helix: 0.13 (0.73), residues: 47 sheet: 0.55 (0.80), residues: 26 loop : -0.75 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 42 TYR 0.016 0.003 TYR B 94 PHE 0.018 0.004 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.49 (13558) covalent geometry : angle 0.79826 / 0.42 (20928) hydrogen bonds : bond 0.11145 / 11.80 ( 512) hydrogen bonds : angle 2.61992 / 3.31 ( 901) ********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.117 Fit side-chains REVERT: B 19 GLN cc_start: 0.9013 (mp10) cc_final: 0.8595 (mt0) outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.7505 time to fit residues: 15.9816 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.098684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060806 restraints weight = 37605.454| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.74 r_work: 0.3143 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13558 Z= 0.275 Angle : 0.610 8.161 20928 Z= 0.346 Chirality : 0.043 0.364 2761 Planarity : 0.005 0.025 689 Dihedral : 26.456 175.296 8368 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.05 % Allowed : 28.28 % 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: 0.44 (0.81), residues: 114 helix: 0.84 (0.79), residues: 47 sheet: 0.72 (0.78), residues: 26 loop : -0.51 (1.15), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 106 TYR 0.006 0.002 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.28 (13558) covalent geometry : angle 0.61008 / 0.35 (20928) hydrogen bonds : bond 0.09296 / 9.86 ( 512) hydrogen bonds : angle 2.50354 / 3.17 ( 901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5305.21 seconds wall clock time: 90 minutes 44.48 seconds (5444.48 seconds total)