Starting phenix.real_space_refine on Tue Feb 3 12:20:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.map" model { file = "/net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hr6_52356/02_2026/9hr6_52356.cif" } resolution = 2.57 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= 0.004 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 600 2.51 5 N 140 2.21 5 O 185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 930 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 186 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.18, per 1000 atoms: 0.19 Number of scatterers: 930 At special positions: 0 Unit cell: (47.5076, 43.9698, 38.9158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 185 8.00 N 140 7.00 C 600 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: 0.07 Conformation dependent library (CDL) restraints added in 35.6 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 200 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.412A pdb=" N LYS A 35 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE B 38 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR A 37 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS B 35 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE C 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 37 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS C 35 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 38 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 37 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS D 35 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE E 38 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR D 37 " --> pdb=" O ILE E 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 6.817A pdb=" N GLY A 43 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 43 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 43 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY D 43 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.14 Time building geometry restraints manager: 0.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 275 1.34 - 1.45: 209 1.45 - 1.57: 451 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 945 Sorted by residual: bond pdb=" C ILE A 54 " pdb=" N GLY A 55 " ideal model delta sigma weight residual 1.329 1.323 0.007 1.19e-02 7.06e+03 3.07e-01 bond pdb=" N GLY D 55 " pdb=" CA GLY D 55 " ideal model delta sigma weight residual 1.449 1.455 -0.006 1.14e-02 7.69e+03 2.81e-01 bond pdb=" C ILE B 54 " pdb=" N GLY B 55 " ideal model delta sigma weight residual 1.329 1.323 0.006 1.19e-02 7.06e+03 2.68e-01 bond pdb=" C ILE E 54 " pdb=" N GLY E 55 " ideal model delta sigma weight residual 1.329 1.323 0.006 1.19e-02 7.06e+03 2.64e-01 bond pdb=" N GLY E 55 " pdb=" CA GLY E 55 " ideal model delta sigma weight residual 1.449 1.455 -0.006 1.14e-02 7.69e+03 2.60e-01 ... (remaining 940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.34: 961 0.34 - 0.69: 190 0.69 - 1.03: 64 1.03 - 1.37: 30 1.37 - 1.72: 25 Bond angle restraints: 1270 Sorted by residual: angle pdb=" N TYR E 39 " pdb=" CA TYR E 39 " pdb=" C TYR E 39 " ideal model delta sigma weight residual 108.76 110.48 -1.72 1.69e+00 3.50e-01 1.03e+00 angle pdb=" N TYR C 39 " pdb=" CA TYR C 39 " pdb=" C TYR C 39 " ideal model delta sigma weight residual 108.76 110.46 -1.70 1.69e+00 3.50e-01 1.01e+00 angle pdb=" N TYR B 39 " pdb=" CA TYR B 39 " pdb=" C TYR B 39 " ideal model delta sigma weight residual 108.76 110.46 -1.70 1.69e+00 3.50e-01 1.01e+00 angle pdb=" N TYR D 39 " pdb=" CA TYR D 39 " pdb=" C TYR D 39 " ideal model delta sigma weight residual 108.76 110.46 -1.70 1.69e+00 3.50e-01 1.01e+00 angle pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" C TYR A 39 " ideal model delta sigma weight residual 108.76 110.44 -1.68 1.69e+00 3.50e-01 9.94e-01 ... (remaining 1265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.59: 435 7.59 - 15.18: 45 15.18 - 22.76: 25 22.76 - 30.35: 10 30.35 - 37.94: 15 Dihedral angle restraints: 530 sinusoidal: 195 harmonic: 335 Sorted by residual: dihedral pdb=" CA ILE C 44 " pdb=" CB ILE C 44 " pdb=" CG1 ILE C 44 " pdb=" CD1 ILE C 44 " ideal model delta sinusoidal sigma weight residual 60.00 97.94 -37.94 3 1.50e+01 4.44e-03 6.66e+00 dihedral pdb=" CA ILE E 44 " pdb=" CB ILE E 44 " pdb=" CG1 ILE E 44 " pdb=" CD1 ILE E 44 " ideal model delta sinusoidal sigma weight residual 60.00 97.94 -37.94 3 1.50e+01 4.44e-03 6.66e+00 dihedral pdb=" CA ILE D 44 " pdb=" CB ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CD1 ILE D 44 " ideal model delta sinusoidal sigma weight residual 60.00 97.94 -37.94 3 1.50e+01 4.44e-03 6.65e+00 ... (remaining 527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 83 0.024 - 0.048: 17 0.048 - 0.071: 10 0.071 - 0.095: 0 0.095 - 0.119: 25 Chirality restraints: 135 Sorted by residual: chirality pdb=" CA ILE D 38 " pdb=" N ILE D 38 " pdb=" C ILE D 38 " pdb=" CB ILE D 38 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA ILE E 38 " pdb=" N ILE E 38 " pdb=" C ILE E 38 " pdb=" CB ILE E 38 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE B 38 " pdb=" N ILE B 38 " pdb=" C ILE B 38 " pdb=" CB ILE B 38 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 132 not shown) Planarity restraints: 155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 51 " -0.001 2.00e-02 2.50e+03 2.53e-03 1.28e-01 pdb=" CG TYR D 51 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR D 51 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 51 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 51 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 51 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " 0.004 2.00e-02 2.50e+03 2.49e-03 1.24e-01 pdb=" CG TYR E 39 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.004 2.00e-02 2.50e+03 2.48e-03 1.23e-01 pdb=" CG TYR A 39 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 152 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 614 3.12 - 3.56: 934 3.56 - 4.01: 1413 4.01 - 4.45: 1770 4.45 - 4.90: 2952 Nonbonded interactions: 7683 Sorted by model distance: nonbonded pdb=" N GLY E 47 " pdb=" O GLY E 47 " model vdw 2.675 2.496 nonbonded pdb=" N GLY C 47 " pdb=" O GLY C 47 " model vdw 2.675 2.496 nonbonded pdb=" N GLY A 47 " pdb=" O GLY A 47 " model vdw 2.675 2.496 nonbonded pdb=" N GLY D 47 " pdb=" O GLY D 47 " model vdw 2.675 2.496 nonbonded pdb=" N GLY B 47 " pdb=" O GLY B 47 " model vdw 2.675 2.496 ... (remaining 7678 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.010 Normalize map: mean=0, sd=1: 32.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 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 : 0.004 0.016 945 Z= 0.163 Angle : 0.407 1.716 1270 Z= 0.248 Chirality : 0.052 0.119 135 Planarity : 0.001 0.003 155 Dihedral : 11.526 37.940 330 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -0.24 (0.84), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.17 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 51 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 945) covalent geometry : angle 0.40662 ( 1270) hydrogen bonds : bond 0.11106 ( 24) hydrogen bonds : angle 6.44722 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.039 Fit side-chains REVERT: A 35 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8054 (ttmm) REVERT: C 35 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7875 (ttmm) REVERT: D 35 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7928 (ttmm) REVERT: E 35 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8277 (ttmm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.5608 time to fit residues: 19.8215 Evaluate side-chains 35 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.151791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.107820 restraints weight = 913.764| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.04 r_work: 0.3512 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 945 Z= 0.124 Angle : 0.391 2.023 1270 Z= 0.234 Chirality : 0.054 0.123 135 Planarity : 0.002 0.006 155 Dihedral : 3.396 13.097 135 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % 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: -0.11 (0.83), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.07 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 945) covalent geometry : angle 0.39082 ( 1270) hydrogen bonds : bond 0.02635 ( 24) hydrogen bonds : angle 4.06743 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.042 Fit side-chains REVERT: A 35 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7766 (ttmm) REVERT: C 35 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7583 (ttmm) REVERT: D 35 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7670 (ttmm) REVERT: E 35 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8162 (ttmm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.4670 time to fit residues: 16.5321 Evaluate side-chains 35 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.148334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104418 restraints weight = 907.157| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.04 r_work: 0.3467 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 945 Z= 0.167 Angle : 0.416 3.464 1270 Z= 0.244 Chirality : 0.053 0.122 135 Planarity : 0.002 0.006 155 Dihedral : 3.487 12.957 135 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.26 % Allowed : 11.58 % Favored : 83.16 % 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: -0.32 (0.80), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.23 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR D 39 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 945) covalent geometry : angle 0.41645 ( 1270) hydrogen bonds : bond 0.02815 ( 24) hydrogen bonds : angle 3.59834 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.041 Fit side-chains REVERT: A 35 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7809 (ttmm) REVERT: C 35 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7628 (ttmm) REVERT: D 35 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7694 (ttmm) REVERT: E 35 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8186 (ttmm) outliers start: 5 outliers final: 0 residues processed: 40 average time/residue: 0.4655 time to fit residues: 18.8244 Evaluate side-chains 35 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.149446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105600 restraints weight = 923.804| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.02 r_work: 0.3484 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 945 Z= 0.148 Angle : 0.430 2.512 1270 Z= 0.254 Chirality : 0.054 0.125 135 Planarity : 0.002 0.006 155 Dihedral : 3.781 15.028 135 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % 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: -0.42 (0.80), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.31 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR A 39 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 945) covalent geometry : angle 0.42971 ( 1270) hydrogen bonds : bond 0.02389 ( 24) hydrogen bonds : angle 3.38307 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.039 Fit side-chains REVERT: A 35 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7808 (ttmm) REVERT: C 35 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7681 (ttmp) REVERT: D 35 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7675 (ttmm) REVERT: E 35 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8184 (ttmm) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4251 time to fit residues: 16.3315 Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.149483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.105176 restraints weight = 953.179| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.08 r_work: 0.3456 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 945 Z= 0.149 Angle : 0.436 2.576 1270 Z= 0.257 Chirality : 0.054 0.127 135 Planarity : 0.002 0.008 155 Dihedral : 3.727 15.467 135 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % 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: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.41 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR C 39 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 945) covalent geometry : angle 0.43564 ( 1270) hydrogen bonds : bond 0.02306 ( 24) hydrogen bonds : angle 3.31935 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.039 Fit side-chains REVERT: A 35 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7787 (ttmm) REVERT: C 35 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7661 (ttmp) REVERT: D 35 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7641 (ttmm) REVERT: E 35 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8139 (ttmm) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4744 time to fit residues: 18.2378 Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.151194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107354 restraints weight = 903.114| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.01 r_work: 0.3501 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 945 Z= 0.137 Angle : 0.441 2.647 1270 Z= 0.260 Chirality : 0.054 0.128 135 Planarity : 0.002 0.007 155 Dihedral : 3.725 15.827 135 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % 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: -0.63 (0.79), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR A 39 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 945) covalent geometry : angle 0.44071 ( 1270) hydrogen bonds : bond 0.02194 ( 24) hydrogen bonds : angle 3.31611 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.039 Fit side-chains REVERT: A 35 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7866 (ttmp) REVERT: C 35 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7683 (ttmp) REVERT: D 35 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7667 (ttmm) REVERT: E 35 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8206 (ttmp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3805 time to fit residues: 15.0216 Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.149891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105444 restraints weight = 924.056| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.08 r_work: 0.3458 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 945 Z= 0.159 Angle : 0.455 2.779 1270 Z= 0.268 Chirality : 0.054 0.130 135 Planarity : 0.002 0.011 155 Dihedral : 3.730 15.476 135 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % 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: -0.78 (0.77), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR E 39 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 945) covalent geometry : angle 0.45540 ( 1270) hydrogen bonds : bond 0.02344 ( 24) hydrogen bonds : angle 3.35834 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.038 Fit side-chains REVERT: A 35 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7845 (ttmp) REVERT: C 35 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7683 (ttmp) REVERT: D 35 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7674 (ttmm) REVERT: E 35 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8197 (ttmp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.3687 time to fit residues: 14.1679 Evaluate side-chains 38 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.150943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106922 restraints weight = 911.777| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.05 r_work: 0.3495 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 945 Z= 0.134 Angle : 0.460 3.227 1270 Z= 0.271 Chirality : 0.054 0.131 135 Planarity : 0.002 0.008 155 Dihedral : 3.722 15.935 135 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % 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: -0.78 (0.76), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR A 39 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 945) covalent geometry : angle 0.46014 ( 1270) hydrogen bonds : bond 0.02102 ( 24) hydrogen bonds : angle 3.28378 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.039 Fit side-chains REVERT: A 35 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7844 (ttmp) REVERT: C 35 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7673 (ttmp) REVERT: D 35 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7649 (ttmm) REVERT: E 35 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8160 (ttmp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3572 time to fit residues: 14.0954 Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106426 restraints weight = 912.626| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.08 r_work: 0.3473 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 945 Z= 0.145 Angle : 0.468 3.324 1270 Z= 0.275 Chirality : 0.054 0.129 135 Planarity : 0.002 0.011 155 Dihedral : 3.769 16.010 135 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 18.95 % Favored : 81.05 % 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 (0.75), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.027 0.002 TYR E 39 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 945) covalent geometry : angle 0.46791 ( 1270) hydrogen bonds : bond 0.02162 ( 24) hydrogen bonds : angle 3.32081 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.036 Fit side-chains REVERT: A 35 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7829 (ttmp) REVERT: C 35 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7670 (ttmp) REVERT: D 35 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7658 (ttmm) REVERT: E 35 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8150 (ttmp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3418 time to fit residues: 13.4934 Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108962 restraints weight = 933.778| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.10 r_work: 0.3514 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 945 Z= 0.120 Angle : 0.466 3.800 1270 Z= 0.274 Chirality : 0.054 0.130 135 Planarity : 0.002 0.009 155 Dihedral : 3.756 16.238 135 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 18.95 % Favored : 81.05 % 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: -0.85 (0.76), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR A 39 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 945) covalent geometry : angle 0.46591 ( 1270) hydrogen bonds : bond 0.01918 ( 24) hydrogen bonds : angle 3.25940 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.022 Fit side-chains REVERT: A 35 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7836 (ttmp) REVERT: C 35 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7647 (ttmp) REVERT: D 35 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7668 (ttmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3187 time to fit residues: 12.5645 Evaluate side-chains 39 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108030 restraints weight = 909.815| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.08 r_work: 0.3499 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 945 Z= 0.140 Angle : 0.473 3.303 1270 Z= 0.278 Chirality : 0.055 0.133 135 Planarity : 0.002 0.011 155 Dihedral : 3.798 15.890 135 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 21.05 % Favored : 78.95 % 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: -0.92 (0.75), residues: 110 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR E 39 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 945) covalent geometry : angle 0.47322 ( 1270) hydrogen bonds : bond 0.02117 ( 24) hydrogen bonds : angle 3.31120 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 935.62 seconds wall clock time: 17 minutes 8.06 seconds (1028.06 seconds total)