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/9kal_62212/02_2026/9kal_62212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kal_62212/02_2026/9kal_62212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kal_62212/02_2026/9kal_62212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kal_62212/02_2026/9kal_62212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kal_62212/02_2026/9kal_62212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kal_62212/02_2026/9kal_62212.map" } resolution = 3.36 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= 0.002 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: 3 Type Number sf(0) Gaussians C 837 2.51 5 N 231 2.21 5 O 270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 1338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 446 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.38, per 1000 atoms: 0.28 Number of scatterers: 1338 At special positions: 0 Unit cell: (77.19, 64.74, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 270 8.00 N 231 7.00 C 837 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: 0.10 Conformation dependent library (CDL) restraints added in 40.6 milliseconds 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 58 removed outlier: 9.038A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N THR B 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N ALA B 56 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS B 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA A 57 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N THR C 54 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N THR B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N ALA C 56 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LYS C 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA B 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.484A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.525A pdb=" N THR A 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.561A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.892A pdb=" N GLY B 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) 14 hydrogen bonds defined for protein. 42 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: 0.12 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 234 1.29 - 1.35: 210 1.35 - 1.42: 51 1.42 - 1.48: 219 1.48 - 1.54: 630 Bond restraints: 1344 Sorted by residual: bond pdb=" CA VAL B 37 " pdb=" CB VAL B 37 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 5.94e-01 bond pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta sigma weight residual 1.466 1.456 0.010 1.36e-02 5.41e+03 5.83e-01 bond pdb=" CA VAL C 37 " pdb=" CB VAL C 37 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.56e-01 bond pdb=" N LYS C 43 " pdb=" CA LYS C 43 " ideal model delta sigma weight residual 1.466 1.457 0.010 1.36e-02 5.41e+03 5.37e-01 bond pdb=" CA VAL A 37 " pdb=" CB VAL A 37 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.36e-01 ... (remaining 1339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 1449 0.61 - 1.23: 271 1.23 - 1.84: 85 1.84 - 2.46: 10 2.46 - 3.07: 6 Bond angle restraints: 1821 Sorted by residual: angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.21 119.14 3.07 1.62e+00 3.81e-01 3.60e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.21 119.20 3.01 1.62e+00 3.81e-01 3.44e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.21 119.22 2.99 1.62e+00 3.81e-01 3.41e+00 angle pdb=" N GLY C 41 " pdb=" CA GLY C 41 " pdb=" C GLY C 41 " ideal model delta sigma weight residual 112.81 110.69 2.12 1.38e+00 5.25e-01 2.37e+00 angle pdb=" N GLY B 41 " pdb=" CA GLY B 41 " pdb=" C GLY B 41 " ideal model delta sigma weight residual 112.81 110.69 2.12 1.38e+00 5.25e-01 2.35e+00 ... (remaining 1816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 719 17.83 - 35.66: 58 35.66 - 53.49: 6 53.49 - 71.33: 6 71.33 - 89.16: 3 Dihedral angle restraints: 792 sinusoidal: 264 harmonic: 528 Sorted by residual: dihedral pdb=" CA SER B 42 " pdb=" C SER B 42 " pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER C 42 " pdb=" C SER C 42 " pdb=" N LYS C 43 " pdb=" CA LYS C 43 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER A 42 " pdb=" C SER A 42 " pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 789 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 120 0.027 - 0.054: 62 0.054 - 0.081: 16 0.081 - 0.108: 27 0.108 - 0.134: 18 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 240 not shown) Planarity restraints: 225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.009 2.00e-02 2.50e+03 7.33e-03 8.06e-01 pdb=" CG HIS A 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.009 2.00e-02 2.50e+03 7.31e-03 8.01e-01 pdb=" CG HIS B 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " 0.009 2.00e-02 2.50e+03 7.26e-03 7.91e-01 pdb=" CG HIS C 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " 0.004 2.00e-02 2.50e+03 ... (remaining 222 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 208 2.79 - 3.31: 1208 3.31 - 3.84: 2095 3.84 - 4.37: 2300 4.37 - 4.90: 4596 Nonbonded interactions: 10407 Sorted by model distance: nonbonded pdb=" ND1 HIS B 50 " pdb=" OD2 ASP B 51 " model vdw 2.257 3.120 nonbonded pdb=" ND1 HIS A 50 " pdb=" OD2 ASP A 51 " model vdw 2.258 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD2 ASP C 51 " model vdw 2.258 3.120 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.322 3.040 nonbonded pdb=" O THR A 59 " pdb=" OG1 THR A 59 " model vdw 2.322 3.040 ... (remaining 10402 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' } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.080 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1344 Z= 0.181 Angle : 0.576 3.072 1821 Z= 0.371 Chirality : 0.052 0.134 243 Planarity : 0.002 0.007 225 Dihedral : 15.785 89.157 456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.42), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.32), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.005 0.001 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 1344) covalent geometry : angle 0.57560 ( 1821) hydrogen bonds : bond 0.09059 ( 14) hydrogen bonds : angle 5.95594 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0485 Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.130568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.109598 restraints weight = 1496.072| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.59 r_work: 0.3940 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1344 Z= 0.156 Angle : 0.448 2.897 1821 Z= 0.271 Chirality : 0.054 0.137 243 Planarity : 0.002 0.008 225 Dihedral : 5.532 18.519 192 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.50), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.006 0.001 PHE C 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 1344) covalent geometry : angle 0.44793 ( 1821) hydrogen bonds : bond 0.01491 ( 14) hydrogen bonds : angle 4.09812 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0469 Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.136913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.115552 restraints weight = 1467.269| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.52 r_work: 0.3769 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1344 Z= 0.212 Angle : 0.480 3.541 1821 Z= 0.294 Chirality : 0.054 0.140 243 Planarity : 0.002 0.010 225 Dihedral : 5.818 19.869 192 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.53), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 39 PHE 0.006 0.001 PHE C 94 HIS 0.008 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 1344) covalent geometry : angle 0.47958 ( 1821) hydrogen bonds : bond 0.01683 ( 14) hydrogen bonds : angle 3.36788 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.1345 Evaluate side-chains 1 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.129872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.109253 restraints weight = 1532.329| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.65 r_work: 0.3827 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1344 Z= 0.130 Angle : 0.411 2.608 1821 Z= 0.250 Chirality : 0.052 0.134 243 Planarity : 0.001 0.007 225 Dihedral : 5.290 17.345 192 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.55), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 39 PHE 0.004 0.001 PHE C 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 1344) covalent geometry : angle 0.41095 ( 1821) hydrogen bonds : bond 0.01144 ( 14) hydrogen bonds : angle 3.11428 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0452 time to fit residues: 0.1298 Evaluate side-chains 1 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.135914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.115357 restraints weight = 1477.225| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.50 r_work: 0.3839 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1344 Z= 0.146 Angle : 0.414 2.856 1821 Z= 0.252 Chirality : 0.052 0.135 243 Planarity : 0.002 0.008 225 Dihedral : 5.215 16.494 192 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.57), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.004 0.001 PHE C 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 1344) covalent geometry : angle 0.41393 ( 1821) hydrogen bonds : bond 0.01164 ( 14) hydrogen bonds : angle 3.05762 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0448 time to fit residues: 0.1825 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.143797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.123565 restraints weight = 1427.386| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.40 r_work: 0.4008 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1344 Z= 0.099 Angle : 0.373 2.316 1821 Z= 0.226 Chirality : 0.051 0.131 243 Planarity : 0.001 0.006 225 Dihedral : 4.840 15.578 192 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.003 0.001 PHE C 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 1344) covalent geometry : angle 0.37319 ( 1821) hydrogen bonds : bond 0.00974 ( 14) hydrogen bonds : angle 3.03434 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0275 time to fit residues: 0.1206 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.133161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.112690 restraints weight = 1464.145| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.51 r_work: 0.3908 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1344 Z= 0.141 Angle : 0.397 2.782 1821 Z= 0.243 Chirality : 0.052 0.134 243 Planarity : 0.001 0.008 225 Dihedral : 4.993 15.569 192 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.59), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.004 0.001 PHE C 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 1344) covalent geometry : angle 0.39727 ( 1821) hydrogen bonds : bond 0.01138 ( 14) hydrogen bonds : angle 3.04771 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0278 time to fit residues: 0.1119 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.143166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.122937 restraints weight = 1408.005| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.43 r_work: 0.3997 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1344 Z= 0.100 Angle : 0.366 2.188 1821 Z= 0.222 Chirality : 0.051 0.130 243 Planarity : 0.001 0.006 225 Dihedral : 4.711 14.216 192 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.59), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.003 0.001 PHE C 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 1344) covalent geometry : angle 0.36605 ( 1821) hydrogen bonds : bond 0.00982 ( 14) hydrogen bonds : angle 3.00695 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0449 time to fit residues: 0.2339 Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.133097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.112531 restraints weight = 1450.668| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.50 r_work: 0.3859 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1344 Z= 0.141 Angle : 0.394 2.779 1821 Z= 0.241 Chirality : 0.052 0.133 243 Planarity : 0.001 0.008 225 Dihedral : 4.907 14.854 192 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.59), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.004 0.001 PHE C 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1344) covalent geometry : angle 0.39396 ( 1821) hydrogen bonds : bond 0.01140 ( 14) hydrogen bonds : angle 3.03370 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0435 time to fit residues: 0.2259 Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.108465 restraints weight = 1545.771| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.61 r_work: 0.3741 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1344 Z= 0.234 Angle : 0.469 3.842 1821 Z= 0.290 Chirality : 0.054 0.137 243 Planarity : 0.002 0.010 225 Dihedral : 5.523 18.181 192 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 39 PHE 0.006 0.002 PHE C 94 HIS 0.008 0.005 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 1344) covalent geometry : angle 0.46896 ( 1821) hydrogen bonds : bond 0.01612 ( 14) hydrogen bonds : angle 3.14877 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0252 time to fit residues: 0.1620 Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.110589 restraints weight = 1514.997| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.64 r_work: 0.3974 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1344 Z= 0.090 Angle : 0.365 2.253 1821 Z= 0.222 Chirality : 0.051 0.132 243 Planarity : 0.001 0.006 225 Dihedral : 4.718 14.332 192 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.59), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR A 39 PHE 0.003 0.001 PHE C 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 1344) covalent geometry : angle 0.36510 ( 1821) hydrogen bonds : bond 0.00940 ( 14) hydrogen bonds : angle 2.99929 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 547.69 seconds wall clock time: 10 minutes 24.64 seconds (624.64 seconds total)