Starting phenix.real_space_refine on Tue Mar 3 11:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.map" model { file = "/net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fb_67622/03_2026/21fb_67622.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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 12 5.16 5 C 1956 2.51 5 N 504 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3012 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: H, A, B, D, E, F, G, I, J, K, L Time building chain proxies: 0.30, per 1000 atoms: 0.10 Number of scatterers: 3012 At special positions: 0 Unit cell: (69.9, 81.084, 48.464, 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 12 16.00 O 540 8.00 N 504 7.00 C 1956 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: 0.24 Conformation dependent library (CDL) restraints added in 119.8 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.415A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 18 through 20 removed outlier: 6.902A pdb=" N PHE G 19 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE E 19 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE C 19 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE I 19 " --> pdb=" O PHE K 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 30 through 32 removed outlier: 6.205A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 30 through 32 removed outlier: 6.205A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU C 34 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET A 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 34 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET I 35 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 36 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU I 34 " --> pdb=" O GLY K 33 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET K 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL I 36 " --> pdb=" O MET K 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.376A pdb=" N VAL E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.353A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL H 12 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 18 through 20 removed outlier: 6.913A pdb=" N PHE F 19 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE D 19 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE B 19 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE H 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE J 19 " --> pdb=" O PHE L 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.164A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N MET D 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N VAL D 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N MET B 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE H 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY H 33 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL B 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N MET H 35 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA J 30 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.164A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N MET D 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N VAL D 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N MET B 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE H 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY H 33 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL B 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N MET H 35 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL J 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET H 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET J 35 " --> pdb=" O VAL L 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 39 through 41 removed outlier: 6.310A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL H 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 102 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: 0.41 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 516 1.30 - 1.42: 780 1.42 - 1.55: 1728 1.55 - 1.67: 12 1.67 - 1.80: 24 Bond restraints: 3060 Sorted by residual: bond pdb=" C GLY E 9 " pdb=" O GLY E 9 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C GLY I 9 " pdb=" O GLY I 9 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C GLY J 9 " pdb=" O GLY J 9 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" C GLY A 9 " pdb=" O GLY A 9 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" C GLY H 9 " pdb=" O GLY H 9 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 3055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 3722 1.10 - 2.21: 333 2.21 - 3.31: 13 3.31 - 4.42: 0 4.42 - 5.52: 48 Bond angle restraints: 4116 Sorted by residual: angle pdb=" C GLY E 9 " pdb=" N TYR E 10 " pdb=" CA TYR E 10 " ideal model delta sigma weight residual 122.37 117.66 4.71 1.72e+00 3.38e-01 7.50e+00 angle pdb=" C GLY G 9 " pdb=" N TYR G 10 " pdb=" CA TYR G 10 " ideal model delta sigma weight residual 122.37 117.67 4.70 1.72e+00 3.38e-01 7.46e+00 angle pdb=" C GLY J 9 " pdb=" N TYR J 10 " pdb=" CA TYR J 10 " ideal model delta sigma weight residual 122.37 117.70 4.67 1.72e+00 3.38e-01 7.36e+00 angle pdb=" C GLY L 9 " pdb=" N TYR L 10 " pdb=" CA TYR L 10 " ideal model delta sigma weight residual 122.37 117.71 4.66 1.72e+00 3.38e-01 7.33e+00 angle pdb=" C GLY C 9 " pdb=" N TYR C 10 " pdb=" CA TYR C 10 " ideal model delta sigma weight residual 122.37 117.71 4.66 1.72e+00 3.38e-01 7.33e+00 ... (remaining 4111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.46: 1438 10.46 - 20.91: 158 20.91 - 31.37: 60 31.37 - 41.83: 24 41.83 - 52.28: 24 Dihedral angle restraints: 1704 sinusoidal: 624 harmonic: 1080 Sorted by residual: dihedral pdb=" CA GLU I 22 " pdb=" C GLU I 22 " pdb=" N ASP I 23 " pdb=" CA ASP I 23 " ideal model delta harmonic sigma weight residual -180.00 -166.47 -13.53 0 5.00e+00 4.00e-02 7.33e+00 dihedral pdb=" CA GLU H 22 " pdb=" C GLU H 22 " pdb=" N ASP H 23 " pdb=" CA ASP H 23 " ideal model delta harmonic sigma weight residual -180.00 -166.47 -13.53 0 5.00e+00 4.00e-02 7.32e+00 dihedral pdb=" CA GLU B 22 " pdb=" C GLU B 22 " pdb=" N ASP B 23 " pdb=" CA ASP B 23 " ideal model delta harmonic sigma weight residual 180.00 -166.49 -13.51 0 5.00e+00 4.00e-02 7.30e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 148 0.027 - 0.053: 145 0.053 - 0.079: 79 0.079 - 0.105: 36 0.105 - 0.131: 60 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILE E 32 " pdb=" N ILE E 32 " pdb=" C ILE E 32 " pdb=" CB ILE E 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE G 32 " pdb=" N ILE G 32 " pdb=" C ILE G 32 " pdb=" CB ILE G 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE H 32 " pdb=" N ILE H 32 " pdb=" C ILE H 32 " pdb=" CB ILE H 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 465 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 9 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C GLY C 9 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY C 9 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR C 10 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 9 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C GLY L 9 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY L 9 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR L 10 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 9 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.89e+00 pdb=" C GLY E 9 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY E 9 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR E 10 " 0.019 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 2187 3.08 - 3.53: 3028 3.53 - 3.99: 4723 3.99 - 4.44: 5265 4.44 - 4.90: 10767 Nonbonded interactions: 25970 Sorted by model distance: nonbonded pdb=" O ASP F 23 " pdb=" OD1 ASP F 23 " model vdw 2.621 3.040 nonbonded pdb=" O ASP G 23 " pdb=" OD1 ASP G 23 " model vdw 2.621 3.040 nonbonded pdb=" O ASP D 23 " pdb=" OD1 ASP D 23 " model vdw 2.621 3.040 nonbonded pdb=" O ASP K 23 " pdb=" OD1 ASP K 23 " model vdw 2.621 3.040 nonbonded pdb=" O ASP E 23 " pdb=" OD1 ASP E 23 " model vdw 2.621 3.040 ... (remaining 25965 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.190 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.007 0.054 3060 Z= 0.345 Angle : 0.800 5.524 4116 Z= 0.459 Chirality : 0.061 0.131 468 Planarity : 0.005 0.032 528 Dihedral : 13.664 52.285 1032 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -1.62 (0.41), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 10 PHE 0.008 0.002 PHE F 20 HIS 0.002 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00686 ( 3060) covalent geometry : angle 0.80002 ( 4116) hydrogen bonds : bond 0.10380 ( 34) hydrogen bonds : angle 7.12251 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.110 Fit side-chains REVERT: B 23 ASP cc_start: 0.8428 (t0) cc_final: 0.8171 (t0) REVERT: G 16 LYS cc_start: 0.8164 (mttt) cc_final: 0.7730 (mtmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0411 time to fit residues: 3.1591 Evaluate side-chains 53 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123395 restraints weight = 4850.453| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.68 r_work: 0.3843 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3060 Z= 0.127 Angle : 0.484 3.888 4116 Z= 0.267 Chirality : 0.058 0.127 468 Planarity : 0.002 0.011 528 Dihedral : 4.626 14.242 420 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 4.33 % Allowed : 14.67 % Favored : 81.00 % 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: -1.09 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.008 0.001 PHE E 20 HIS 0.002 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3060) covalent geometry : angle 0.48371 ( 4116) hydrogen bonds : bond 0.02343 ( 34) hydrogen bonds : angle 5.79516 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.071 Fit side-chains REVERT: C 23 ASP cc_start: 0.8277 (t0) cc_final: 0.7882 (t0) REVERT: H 23 ASP cc_start: 0.8379 (t0) cc_final: 0.8040 (t0) REVERT: A 23 ASP cc_start: 0.8381 (t0) cc_final: 0.8126 (t0) REVERT: B 23 ASP cc_start: 0.8465 (t0) cc_final: 0.8095 (t0) REVERT: F 16 LYS cc_start: 0.8495 (mttt) cc_final: 0.7776 (tttp) REVERT: F 23 ASP cc_start: 0.7846 (t0) cc_final: 0.7563 (t0) REVERT: G 16 LYS cc_start: 0.8308 (mttt) cc_final: 0.7832 (mtmm) outliers start: 13 outliers final: 2 residues processed: 68 average time/residue: 0.0425 time to fit residues: 3.8526 Evaluate side-chains 56 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain K residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.135954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118349 restraints weight = 4880.854| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.67 r_work: 0.3750 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3060 Z= 0.219 Angle : 0.560 4.377 4116 Z= 0.310 Chirality : 0.059 0.128 468 Planarity : 0.002 0.013 528 Dihedral : 4.872 14.893 420 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.00 % Allowed : 16.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 10 PHE 0.008 0.001 PHE C 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 3060) covalent geometry : angle 0.55995 ( 4116) hydrogen bonds : bond 0.03083 ( 34) hydrogen bonds : angle 5.49922 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.112 Fit side-chains REVERT: H 23 ASP cc_start: 0.8435 (t0) cc_final: 0.8191 (t0) REVERT: A 23 ASP cc_start: 0.8523 (t0) cc_final: 0.8189 (t0) REVERT: B 23 ASP cc_start: 0.8501 (t0) cc_final: 0.8129 (t0) REVERT: E 16 LYS cc_start: 0.8392 (mttt) cc_final: 0.7553 (tttp) REVERT: F 23 ASP cc_start: 0.7957 (t0) cc_final: 0.7624 (t0) REVERT: G 16 LYS cc_start: 0.8500 (mttt) cc_final: 0.7976 (mtmm) REVERT: G 23 ASP cc_start: 0.7945 (t0) cc_final: 0.7554 (t0) REVERT: I 23 ASP cc_start: 0.8418 (t0) cc_final: 0.8139 (t0) REVERT: J 23 ASP cc_start: 0.8604 (t0) cc_final: 0.8286 (t0) REVERT: K 23 ASP cc_start: 0.8479 (t0) cc_final: 0.8215 (t0) REVERT: L 23 ASP cc_start: 0.8522 (t0) cc_final: 0.8132 (t0) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.0453 time to fit residues: 3.9881 Evaluate side-chains 59 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.119935 restraints weight = 4943.444| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.58 r_work: 0.3764 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3060 Z= 0.189 Angle : 0.540 4.943 4116 Z= 0.292 Chirality : 0.059 0.126 468 Planarity : 0.002 0.011 528 Dihedral : 4.736 14.740 420 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.67 % Allowed : 16.33 % Favored : 80.00 % 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: -1.05 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR I 10 PHE 0.006 0.001 PHE E 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 3060) covalent geometry : angle 0.54013 ( 4116) hydrogen bonds : bond 0.02666 ( 34) hydrogen bonds : angle 5.30965 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.122 Fit side-chains REVERT: H 16 LYS cc_start: 0.8323 (mttt) cc_final: 0.7951 (ttmm) REVERT: A 23 ASP cc_start: 0.8496 (t0) cc_final: 0.8121 (t0) REVERT: B 23 ASP cc_start: 0.8542 (t0) cc_final: 0.8302 (t0) REVERT: E 16 LYS cc_start: 0.8365 (mttt) cc_final: 0.7651 (mtmm) REVERT: F 23 ASP cc_start: 0.7953 (t0) cc_final: 0.7641 (t0) REVERT: G 16 LYS cc_start: 0.8529 (mttt) cc_final: 0.7993 (mtmm) REVERT: G 23 ASP cc_start: 0.7992 (t0) cc_final: 0.7521 (t0) REVERT: I 11 GLU cc_start: 0.8676 (tt0) cc_final: 0.8425 (tt0) REVERT: I 23 ASP cc_start: 0.8387 (t0) cc_final: 0.8185 (t0) REVERT: J 23 ASP cc_start: 0.8657 (t0) cc_final: 0.8393 (t0) REVERT: K 23 ASP cc_start: 0.8484 (t0) cc_final: 0.8223 (t0) REVERT: L 23 ASP cc_start: 0.8557 (t0) cc_final: 0.8213 (t0) outliers start: 11 outliers final: 3 residues processed: 68 average time/residue: 0.0584 time to fit residues: 4.9678 Evaluate side-chains 60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.130838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.114520 restraints weight = 4952.090| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.59 r_work: 0.3720 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3060 Z= 0.251 Angle : 0.598 4.377 4116 Z= 0.325 Chirality : 0.060 0.130 468 Planarity : 0.002 0.011 528 Dihedral : 5.023 14.449 420 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.00 % Allowed : 18.33 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.007 0.001 PHE E 19 HIS 0.003 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 3060) covalent geometry : angle 0.59762 ( 4116) hydrogen bonds : bond 0.02985 ( 34) hydrogen bonds : angle 5.32677 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.090 Fit side-chains REVERT: C 23 ASP cc_start: 0.8286 (t0) cc_final: 0.8061 (t0) REVERT: H 16 LYS cc_start: 0.8411 (mttt) cc_final: 0.7992 (ttmm) REVERT: A 23 ASP cc_start: 0.8464 (t0) cc_final: 0.8216 (t0) REVERT: E 16 LYS cc_start: 0.8512 (mttt) cc_final: 0.7816 (mtmm) REVERT: E 23 ASP cc_start: 0.8125 (t0) cc_final: 0.7884 (t0) REVERT: F 23 ASP cc_start: 0.7974 (t0) cc_final: 0.7645 (t0) REVERT: I 11 GLU cc_start: 0.8709 (tt0) cc_final: 0.8429 (tt0) REVERT: J 23 ASP cc_start: 0.8650 (t0) cc_final: 0.8450 (t0) REVERT: K 23 ASP cc_start: 0.8475 (t0) cc_final: 0.8237 (t0) REVERT: L 23 ASP cc_start: 0.8533 (t0) cc_final: 0.8220 (t0) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.0523 time to fit residues: 4.4476 Evaluate side-chains 61 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain K residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.129019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.112581 restraints weight = 5046.838| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.59 r_work: 0.3690 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3060 Z= 0.292 Angle : 0.657 5.879 4116 Z= 0.353 Chirality : 0.060 0.133 468 Planarity : 0.002 0.015 528 Dihedral : 5.186 15.379 420 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.33 % Allowed : 18.00 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.012 0.001 PHE A 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 3060) covalent geometry : angle 0.65668 ( 4116) hydrogen bonds : bond 0.03066 ( 34) hydrogen bonds : angle 5.36916 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.132 Fit side-chains REVERT: C 23 ASP cc_start: 0.8333 (t0) cc_final: 0.8062 (t0) REVERT: H 16 LYS cc_start: 0.8449 (mttt) cc_final: 0.8045 (ttmm) REVERT: A 11 GLU cc_start: 0.8773 (tt0) cc_final: 0.8545 (tt0) REVERT: E 16 LYS cc_start: 0.8523 (mttt) cc_final: 0.7806 (mtmm) REVERT: E 23 ASP cc_start: 0.8129 (t0) cc_final: 0.7883 (t0) REVERT: F 23 ASP cc_start: 0.7976 (t0) cc_final: 0.7612 (t0) REVERT: G 16 LYS cc_start: 0.8600 (mttt) cc_final: 0.8058 (mtmm) REVERT: I 11 GLU cc_start: 0.8768 (tt0) cc_final: 0.8489 (tt0) REVERT: L 23 ASP cc_start: 0.8578 (t0) cc_final: 0.8345 (t0) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.0588 time to fit residues: 5.0115 Evaluate side-chains 60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.134366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.117779 restraints weight = 4922.708| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.62 r_work: 0.3781 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3060 Z= 0.182 Angle : 0.573 4.904 4116 Z= 0.316 Chirality : 0.058 0.130 468 Planarity : 0.003 0.020 528 Dihedral : 4.802 14.597 420 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.67 % Allowed : 18.00 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR H 10 PHE 0.011 0.001 PHE A 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3060) covalent geometry : angle 0.57337 ( 4116) hydrogen bonds : bond 0.02714 ( 34) hydrogen bonds : angle 5.24488 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.112 Fit side-chains REVERT: C 23 ASP cc_start: 0.8211 (t0) cc_final: 0.7801 (t0) REVERT: H 16 LYS cc_start: 0.8360 (mttt) cc_final: 0.7960 (ttmm) REVERT: H 35 MET cc_start: 0.8744 (ttp) cc_final: 0.8239 (ttp) REVERT: E 16 LYS cc_start: 0.8428 (mttt) cc_final: 0.7536 (tttp) REVERT: F 23 ASP cc_start: 0.7971 (t0) cc_final: 0.7627 (t0) REVERT: G 16 LYS cc_start: 0.8561 (mttt) cc_final: 0.7965 (mtmm) REVERT: G 23 ASP cc_start: 0.7855 (t0) cc_final: 0.7412 (t0) REVERT: G 24 VAL cc_start: 0.8829 (t) cc_final: 0.8601 (p) REVERT: I 11 GLU cc_start: 0.8768 (tt0) cc_final: 0.8473 (tt0) REVERT: I 32 ILE cc_start: 0.9393 (mm) cc_final: 0.9181 (mm) REVERT: L 23 ASP cc_start: 0.8461 (t0) cc_final: 0.8257 (t0) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.0585 time to fit residues: 5.3613 Evaluate side-chains 66 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.134500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.117950 restraints weight = 4925.019| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.56 r_work: 0.3785 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3060 Z= 0.205 Angle : 0.620 6.402 4116 Z= 0.334 Chirality : 0.059 0.140 468 Planarity : 0.003 0.020 528 Dihedral : 4.943 16.338 420 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.00 % Allowed : 20.00 % Favored : 78.00 % 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: -1.32 (0.43), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 10 PHE 0.013 0.001 PHE A 19 HIS 0.003 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 3060) covalent geometry : angle 0.61968 ( 4116) hydrogen bonds : bond 0.02761 ( 34) hydrogen bonds : angle 5.25006 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.116 Fit side-chains REVERT: C 23 ASP cc_start: 0.8140 (t0) cc_final: 0.7869 (t0) REVERT: H 16 LYS cc_start: 0.8368 (mttt) cc_final: 0.7980 (ttmm) REVERT: E 16 LYS cc_start: 0.8437 (mttt) cc_final: 0.7733 (mtmm) REVERT: E 23 ASP cc_start: 0.8062 (t0) cc_final: 0.7815 (t0) REVERT: F 23 ASP cc_start: 0.7985 (t0) cc_final: 0.7606 (t0) REVERT: G 16 LYS cc_start: 0.8577 (mttt) cc_final: 0.7985 (mtmm) REVERT: G 23 ASP cc_start: 0.7890 (t0) cc_final: 0.7538 (t0) REVERT: I 11 GLU cc_start: 0.8709 (tt0) cc_final: 0.8428 (tt0) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.0439 time to fit residues: 4.2804 Evaluate side-chains 67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.143700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126780 restraints weight = 4818.104| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.63 r_work: 0.3938 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3060 Z= 0.140 Angle : 0.604 6.210 4116 Z= 0.326 Chirality : 0.058 0.168 468 Planarity : 0.004 0.023 528 Dihedral : 4.708 13.906 420 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 2.00 % Allowed : 22.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.44), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR H 10 PHE 0.013 0.001 PHE A 19 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3060) covalent geometry : angle 0.60391 ( 4116) hydrogen bonds : bond 0.02308 ( 34) hydrogen bonds : angle 5.10696 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.116 Fit side-chains REVERT: C 23 ASP cc_start: 0.8135 (t0) cc_final: 0.7908 (t0) REVERT: H 16 LYS cc_start: 0.8311 (mttt) cc_final: 0.7934 (ttmm) REVERT: H 35 MET cc_start: 0.8554 (ttp) cc_final: 0.8328 (ttp) REVERT: E 16 LYS cc_start: 0.8321 (mttt) cc_final: 0.7459 (tttp) REVERT: E 23 ASP cc_start: 0.8018 (t0) cc_final: 0.7768 (t0) REVERT: F 23 ASP cc_start: 0.7929 (t0) cc_final: 0.7562 (t0) REVERT: G 16 LYS cc_start: 0.8537 (mttt) cc_final: 0.7936 (mtmm) REVERT: G 23 ASP cc_start: 0.7899 (t0) cc_final: 0.7530 (t0) REVERT: I 11 GLU cc_start: 0.8701 (tt0) cc_final: 0.8449 (tt0) outliers start: 6 outliers final: 1 residues processed: 70 average time/residue: 0.0519 time to fit residues: 4.5426 Evaluate side-chains 62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.131606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114853 restraints weight = 4918.876| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.57 r_work: 0.3733 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 3060 Z= 0.288 Angle : 0.748 6.345 4116 Z= 0.398 Chirality : 0.059 0.136 468 Planarity : 0.004 0.027 528 Dihedral : 5.153 15.159 420 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.67 % Allowed : 20.67 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.43), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.014 0.001 PHE A 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 3060) covalent geometry : angle 0.74814 ( 4116) hydrogen bonds : bond 0.02991 ( 34) hydrogen bonds : angle 5.35206 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.069 Fit side-chains REVERT: C 23 ASP cc_start: 0.8251 (t0) cc_final: 0.7997 (t0) REVERT: H 16 LYS cc_start: 0.8418 (mttt) cc_final: 0.7994 (ttmm) REVERT: E 23 ASP cc_start: 0.8069 (t0) cc_final: 0.7811 (t0) REVERT: E 35 MET cc_start: 0.8980 (ptt) cc_final: 0.8774 (ptt) REVERT: F 23 ASP cc_start: 0.7992 (t0) cc_final: 0.7603 (t0) REVERT: F 35 MET cc_start: 0.8736 (ptt) cc_final: 0.8425 (ptt) REVERT: G 16 LYS cc_start: 0.8620 (mttt) cc_final: 0.8035 (mtmm) REVERT: G 23 ASP cc_start: 0.8040 (t0) cc_final: 0.7608 (t0) REVERT: I 11 GLU cc_start: 0.8752 (tt0) cc_final: 0.8479 (tt0) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.0381 time to fit residues: 3.2427 Evaluate side-chains 63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain G residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.0070 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.121369 restraints weight = 4811.079| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.58 r_work: 0.3842 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3060 Z= 0.185 Angle : 0.652 6.060 4116 Z= 0.350 Chirality : 0.058 0.142 468 Planarity : 0.004 0.026 528 Dihedral : 4.884 14.579 420 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 1.00 % Allowed : 21.00 % Favored : 78.00 % 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: -1.20 (0.43), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 10 PHE 0.012 0.001 PHE A 19 HIS 0.002 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3060) covalent geometry : angle 0.65227 ( 4116) hydrogen bonds : bond 0.02501 ( 34) hydrogen bonds : angle 5.29980 ( 102) =============================================================================== Job complete usr+sys time: 672.89 seconds wall clock time: 12 minutes 8.48 seconds (728.48 seconds total)