Starting phenix.real_space_refine on Fri Aug 22 15:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.map" model { file = "/net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ade_15361/08_2025/8ade_15361.cif" } resolution = 2.78 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: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 3255 2.51 5 N 826 2.21 5 O 938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5026 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 0.63, per 1000 atoms: 0.13 Number of scatterers: 5026 At special positions: 0 Unit cell: (68.64, 85.28, 50.96, 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 7 16.00 O 938 8.00 N 826 7.00 C 3255 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: 0.40 Conformation dependent library (CDL) restraints added in 135.2 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.253A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS C 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS D 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 12 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS E 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 12 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS F 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL E 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU F 12 " --> pdb=" O MET G 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS G 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL F 14 " --> pdb=" O LYS G 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.802A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 20 " --> pdb=" O ARG G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.403A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.474A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU B 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU E 72 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU F 72 " --> pdb=" O ILE G 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 7.031A pdb=" N TRP A 79 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP B 79 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 80 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP C 79 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS D 80 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP D 79 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 80 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP E 79 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 80 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP F 79 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS G 80 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AB1, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.486A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 109 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 109 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA D 109 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 109 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA F 109 " --> pdb=" O LEU G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.857A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 114 hydrogen bonds defined for protein. 342 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: 0.68 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 902 1.33 - 1.45: 1317 1.45 - 1.57: 2912 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 5145 Sorted by residual: bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.37e+01 bond pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 bond pdb=" N ILE G 26 " pdb=" CA ILE G 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 ... (remaining 5140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4654 1.46 - 2.91: 1910 2.91 - 4.37: 366 4.37 - 5.83: 42 5.83 - 7.28: 28 Bond angle restraints: 7000 Sorted by residual: angle pdb=" C PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta sigma weight residual 110.95 104.89 6.06 1.31e+00 5.83e-01 2.14e+01 angle pdb=" C PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO A 24 " pdb=" CA PRO A 24 " pdb=" CB PRO A 24 " ideal model delta sigma weight residual 110.95 104.92 6.03 1.31e+00 5.83e-01 2.12e+01 angle pdb=" C PRO D 24 " pdb=" CA PRO D 24 " pdb=" CB PRO D 24 " ideal model delta sigma weight residual 110.95 104.93 6.02 1.31e+00 5.83e-01 2.11e+01 ... (remaining 6995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 2737 11.52 - 23.03: 238 23.03 - 34.55: 42 34.55 - 46.07: 0 46.07 - 57.58: 14 Dihedral angle restraints: 3031 sinusoidal: 1148 harmonic: 1883 Sorted by residual: dihedral pdb=" C PRO C 24 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO B 24 " pdb=" N PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO E 24 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta harmonic sigma weight residual -120.70 -112.67 -8.03 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 3028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 209 0.047 - 0.094: 249 0.094 - 0.141: 203 0.141 - 0.189: 116 0.189 - 0.236: 49 Chirality restraints: 826 Sorted by residual: chirality pdb=" CA ILE F 68 " pdb=" N ILE F 68 " pdb=" C ILE F 68 " pdb=" CB ILE F 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE E 68 " pdb=" N ILE E 68 " pdb=" C ILE E 68 " pdb=" CB ILE E 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 823 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 114 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C TYR C 114 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR C 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C TYR A 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR A 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C TYR E 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR E 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER E 115 " 0.015 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 406 2.75 - 3.29: 5005 3.29 - 3.82: 8088 3.82 - 4.36: 11472 4.36 - 4.90: 20635 Nonbonded interactions: 45606 Sorted by model distance: nonbonded pdb=" O SER A 117 " pdb=" OG SER B 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER D 117 " pdb=" OG SER E 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER C 117 " pdb=" OG SER D 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER B 117 " pdb=" OG SER C 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER F 117 " pdb=" OG SER G 117 " model vdw 2.213 3.040 ... (remaining 45601 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.670 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.730 Find NCS groups from input model: 0.060 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:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.012 0.042 5145 Z= 0.934 Angle : 1.581 7.283 7000 Z= 1.154 Chirality : 0.107 0.236 826 Planarity : 0.005 0.026 861 Dihedral : 9.637 57.583 1813 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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 aren not related in a simple way. whole: -4.12 (0.23), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 34 TYR 0.006 0.001 TYR C 116 PHE 0.004 0.001 PHE G 33 TRP 0.001 0.001 TRP E 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.01226 ( 5145) covalent geometry : angle 1.58126 ( 7000) hydrogen bonds : bond 0.12626 ( 114) hydrogen bonds : angle 7.90723 ( 342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.8874 (m) cc_final: 0.8558 (p) REVERT: C 123 THR cc_start: 0.7245 (t) cc_final: 0.6610 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4900 time to fit residues: 91.3793 Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.158069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134540 restraints weight = 6081.004| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.56 r_work: 0.4061 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5145 Z= 0.180 Angle : 0.659 6.570 7000 Z= 0.348 Chirality : 0.050 0.134 826 Planarity : 0.005 0.043 861 Dihedral : 4.979 15.411 693 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.30 % Allowed : 18.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.25), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 104 TYR 0.015 0.002 TYR E 114 PHE 0.012 0.002 PHE B 33 TRP 0.009 0.001 TRP D 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5145) covalent geometry : angle 0.65874 ( 7000) hydrogen bonds : bond 0.03715 ( 114) hydrogen bonds : angle 6.05079 ( 342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7927 (ttt) cc_final: 0.7522 (tpt) REVERT: B 92 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: B 99 ASP cc_start: 0.7078 (t0) cc_final: 0.6685 (t0) REVERT: D 13 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7311 (tmt) REVERT: D 35 LYS cc_start: 0.8395 (ttmm) cc_final: 0.8025 (ttmm) REVERT: E 21 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7913 (tpp80) REVERT: E 35 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (ttmm) REVERT: F 34 ARG cc_start: 0.8003 (tpt-90) cc_final: 0.7732 (ttt90) REVERT: G 13 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7135 (tmt) REVERT: G 89 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7986 (mt-10) outliers start: 18 outliers final: 5 residues processed: 152 average time/residue: 0.5808 time to fit residues: 91.0037 Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.120227 restraints weight = 6182.767| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.48 r_work: 0.3895 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5145 Z= 0.230 Angle : 0.667 7.332 7000 Z= 0.349 Chirality : 0.050 0.168 826 Planarity : 0.005 0.039 861 Dihedral : 5.324 16.447 693 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % Favored : 76.92 % 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 aren not related in a simple way. whole: -3.02 (0.26), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.019 0.002 TYR F 114 PHE 0.012 0.002 PHE B 33 TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 5145) covalent geometry : angle 0.66738 ( 7000) hydrogen bonds : bond 0.02940 ( 114) hydrogen bonds : angle 5.31124 ( 342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8169 (ttt) cc_final: 0.7813 (tpt) REVERT: A 74 ASP cc_start: 0.9086 (t0) cc_final: 0.8878 (t0) REVERT: B 92 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: B 104 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7918 (ttm110) REVERT: C 92 GLU cc_start: 0.8664 (pt0) cc_final: 0.7683 (tm-30) REVERT: D 13 MET cc_start: 0.7736 (tmt) cc_final: 0.7423 (tmt) REVERT: D 35 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8146 (ttmm) REVERT: E 13 MET cc_start: 0.7796 (tmt) cc_final: 0.6830 (tmt) REVERT: E 21 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7996 (tpp80) REVERT: E 35 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: E 104 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7997 (ttp-110) REVERT: F 21 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7868 (tpp80) REVERT: F 77 SER cc_start: 0.8806 (t) cc_final: 0.8456 (m) REVERT: G 13 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7527 (tmt) REVERT: G 89 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8112 (mt-10) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 0.6684 time to fit residues: 86.5302 Evaluate side-chains 120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.142383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117755 restraints weight = 6206.614| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.52 r_work: 0.3861 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5145 Z= 0.216 Angle : 0.618 6.581 7000 Z= 0.326 Chirality : 0.049 0.129 826 Planarity : 0.005 0.053 861 Dihedral : 5.260 16.867 693 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.30 % Allowed : 20.51 % Favored : 76.19 % 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 aren not related in a simple way. whole: -2.89 (0.27), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 104 TYR 0.016 0.002 TYR C 114 PHE 0.007 0.002 PHE B 33 TRP 0.007 0.002 TRP F 79 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 5145) covalent geometry : angle 0.61843 ( 7000) hydrogen bonds : bond 0.02586 ( 114) hydrogen bonds : angle 5.11898 ( 342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8218 (ttt) cc_final: 0.7849 (tpt) REVERT: B 92 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: B 104 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.7995 (ttm110) REVERT: C 92 GLU cc_start: 0.8619 (pt0) cc_final: 0.7695 (tm-30) REVERT: D 13 MET cc_start: 0.7864 (tmt) cc_final: 0.7467 (tmt) REVERT: D 21 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7782 (mmm-85) REVERT: D 35 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8117 (ttmm) REVERT: D 92 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 13 MET cc_start: 0.7867 (tmt) cc_final: 0.6866 (tmt) REVERT: E 21 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7891 (tpp80) REVERT: F 21 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7835 (tpp80) REVERT: F 35 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8214 (ttmt) REVERT: G 13 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7411 (tmt) REVERT: G 80 LYS cc_start: 0.8388 (tttt) cc_final: 0.8120 (tttm) REVERT: G 99 ASP cc_start: 0.7131 (t70) cc_final: 0.6688 (t70) outliers start: 18 outliers final: 5 residues processed: 121 average time/residue: 0.6805 time to fit residues: 84.6787 Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.143212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.118567 restraints weight = 6201.516| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.52 r_work: 0.3864 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5145 Z= 0.190 Angle : 0.605 6.001 7000 Z= 0.318 Chirality : 0.049 0.153 826 Planarity : 0.005 0.053 861 Dihedral : 5.181 17.032 693 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.48 % Allowed : 21.06 % Favored : 75.46 % 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 aren not related in a simple way. whole: -2.82 (0.27), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 104 TYR 0.014 0.002 TYR C 114 PHE 0.007 0.002 PHE E 64 TRP 0.005 0.001 TRP F 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5145) covalent geometry : angle 0.60459 ( 7000) hydrogen bonds : bond 0.02406 ( 114) hydrogen bonds : angle 4.99359 ( 342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8146 (ttt) cc_final: 0.7788 (tpt) REVERT: A 92 GLU cc_start: 0.8422 (pt0) cc_final: 0.7708 (tm-30) REVERT: B 92 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 104 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7892 (ttm110) REVERT: C 92 GLU cc_start: 0.8584 (pt0) cc_final: 0.7688 (tm-30) REVERT: D 13 MET cc_start: 0.7840 (tmt) cc_final: 0.7459 (tmt) REVERT: D 21 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7741 (mmm-85) REVERT: D 35 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8272 (ttmm) REVERT: D 92 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 13 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6906 (tmt) REVERT: E 21 ARG cc_start: 0.8368 (mmm160) cc_final: 0.7910 (tpp80) REVERT: E 104 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8000 (ttp-110) REVERT: F 21 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7836 (tpp80) REVERT: F 35 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8190 (ttmt) REVERT: G 13 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7492 (tmt) REVERT: G 80 LYS cc_start: 0.8374 (tttt) cc_final: 0.8076 (tttm) outliers start: 19 outliers final: 9 residues processed: 118 average time/residue: 0.7133 time to fit residues: 86.4365 Evaluate side-chains 117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.149869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125953 restraints weight = 5788.257| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.48 r_work: 0.3882 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5145 Z= 0.206 Angle : 0.612 5.590 7000 Z= 0.322 Chirality : 0.050 0.146 826 Planarity : 0.004 0.056 861 Dihedral : 5.201 17.821 693 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.40 % Allowed : 20.70 % Favored : 74.91 % 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 aren not related in a simple way. whole: -2.66 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 104 TYR 0.014 0.002 TYR C 114 PHE 0.007 0.002 PHE G 33 TRP 0.006 0.001 TRP F 79 HIS 0.005 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 5145) covalent geometry : angle 0.61229 ( 7000) hydrogen bonds : bond 0.02390 ( 114) hydrogen bonds : angle 4.91924 ( 342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8201 (ttt) cc_final: 0.7847 (tpt) REVERT: A 92 GLU cc_start: 0.8445 (pt0) cc_final: 0.7657 (tm-30) REVERT: B 92 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 104 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7752 (ttm110) REVERT: C 92 GLU cc_start: 0.8594 (pt0) cc_final: 0.7741 (tm-30) REVERT: D 13 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7503 (tmt) REVERT: D 21 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7663 (mmm-85) REVERT: D 35 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8250 (ttmm) REVERT: D 58 LEU cc_start: 0.8443 (mt) cc_final: 0.8231 (mt) REVERT: D 92 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 13 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6780 (tmt) REVERT: E 21 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7859 (tpp80) REVERT: F 13 MET cc_start: 0.7852 (tmt) cc_final: 0.7409 (tmt) REVERT: F 21 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7766 (tpp80) REVERT: F 35 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8090 (ttmt) REVERT: G 13 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7458 (tmt) REVERT: G 80 LYS cc_start: 0.8235 (tttt) cc_final: 0.7910 (tttm) outliers start: 24 outliers final: 11 residues processed: 122 average time/residue: 0.7054 time to fit residues: 88.2804 Evaluate side-chains 119 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.151523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.127469 restraints weight = 5680.188| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.50 r_work: 0.3912 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5145 Z= 0.175 Angle : 0.605 6.119 7000 Z= 0.316 Chirality : 0.049 0.145 826 Planarity : 0.005 0.057 861 Dihedral : 5.121 17.382 693 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.48 % Allowed : 22.53 % Favored : 73.99 % 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 aren not related in a simple way. whole: -2.64 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 104 TYR 0.013 0.002 TYR C 114 PHE 0.007 0.001 PHE E 64 TRP 0.004 0.001 TRP F 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5145) covalent geometry : angle 0.60512 ( 7000) hydrogen bonds : bond 0.02266 ( 114) hydrogen bonds : angle 4.84253 ( 342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8195 (ttt) cc_final: 0.7818 (tpt) REVERT: A 92 GLU cc_start: 0.8437 (pt0) cc_final: 0.7695 (tm-30) REVERT: B 92 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: B 104 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7767 (ttm110) REVERT: C 92 GLU cc_start: 0.8609 (pt0) cc_final: 0.7737 (tm-30) REVERT: D 13 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7449 (tmt) REVERT: D 21 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7521 (mmm-85) REVERT: D 26 ILE cc_start: 0.8864 (pt) cc_final: 0.8539 (mt) REVERT: D 35 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8228 (ttmm) REVERT: D 58 LEU cc_start: 0.8368 (mt) cc_final: 0.8138 (mt) REVERT: D 92 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7717 (tm-30) REVERT: E 13 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6842 (tmt) REVERT: E 21 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7826 (tpp80) REVERT: F 21 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7746 (tpp80) REVERT: F 35 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8099 (ttmt) REVERT: G 13 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7483 (tmt) REVERT: G 80 LYS cc_start: 0.8176 (tttt) cc_final: 0.7858 (tttm) outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 0.7346 time to fit residues: 88.9479 Evaluate side-chains 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.151355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.127357 restraints weight = 5736.177| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.50 r_work: 0.3911 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5145 Z= 0.186 Angle : 0.614 6.583 7000 Z= 0.322 Chirality : 0.050 0.163 826 Planarity : 0.005 0.071 861 Dihedral : 5.142 17.302 693 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.11 % Allowed : 23.63 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 104 TYR 0.013 0.002 TYR C 114 PHE 0.007 0.001 PHE E 64 TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5145) covalent geometry : angle 0.61435 ( 7000) hydrogen bonds : bond 0.02281 ( 114) hydrogen bonds : angle 4.78940 ( 342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8198 (ttt) cc_final: 0.7851 (tpt) REVERT: A 92 GLU cc_start: 0.8509 (pt0) cc_final: 0.7672 (tm-30) REVERT: B 92 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: B 104 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7790 (ttm110) REVERT: C 92 GLU cc_start: 0.8613 (pt0) cc_final: 0.7760 (tm-30) REVERT: D 13 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7529 (tmt) REVERT: D 21 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7551 (mmm-85) REVERT: D 26 ILE cc_start: 0.8893 (pt) cc_final: 0.8592 (mt) REVERT: D 35 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8261 (ttmm) REVERT: D 92 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 13 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6845 (tmt) REVERT: E 21 ARG cc_start: 0.8321 (mmm160) cc_final: 0.7843 (tpp80) REVERT: F 13 MET cc_start: 0.7832 (tmt) cc_final: 0.7419 (tmt) REVERT: F 21 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7766 (tpp80) REVERT: G 13 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7503 (tmt) REVERT: G 80 LYS cc_start: 0.8201 (tttt) cc_final: 0.7893 (tttm) outliers start: 17 outliers final: 7 residues processed: 113 average time/residue: 0.7067 time to fit residues: 81.9485 Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.124619 restraints weight = 5716.529| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.51 r_work: 0.3881 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5145 Z= 0.233 Angle : 0.647 7.539 7000 Z= 0.339 Chirality : 0.051 0.186 826 Planarity : 0.005 0.067 861 Dihedral : 5.235 17.763 693 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.11 % Allowed : 23.63 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 104 TYR 0.012 0.002 TYR C 114 PHE 0.007 0.001 PHE E 64 TRP 0.006 0.002 TRP E 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 5145) covalent geometry : angle 0.64654 ( 7000) hydrogen bonds : bond 0.02446 ( 114) hydrogen bonds : angle 4.81019 ( 342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8210 (ttt) cc_final: 0.7846 (tpt) REVERT: A 92 GLU cc_start: 0.8512 (pt0) cc_final: 0.7672 (tm-30) REVERT: B 92 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: B 104 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7771 (ttm110) REVERT: C 92 GLU cc_start: 0.8608 (pt0) cc_final: 0.7763 (tm-30) REVERT: D 13 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7535 (tmt) REVERT: D 21 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7530 (mmm-85) REVERT: D 26 ILE cc_start: 0.8887 (pt) cc_final: 0.8571 (mt) REVERT: D 35 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8215 (ttmm) REVERT: D 92 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7875 (tm-30) REVERT: E 13 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6827 (tmt) REVERT: E 21 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7838 (tpp80) REVERT: E 58 LEU cc_start: 0.7940 (tp) cc_final: 0.7717 (tt) REVERT: F 13 MET cc_start: 0.7812 (tmt) cc_final: 0.7365 (tmt) REVERT: F 21 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7765 (tpp80) REVERT: F 104 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8183 (ttm110) REVERT: G 13 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7467 (tmt) REVERT: G 80 LYS cc_start: 0.8238 (tttt) cc_final: 0.7927 (tttm) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.6524 time to fit residues: 75.0332 Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.130986 restraints weight = 5580.353| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.48 r_work: 0.3947 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5145 Z= 0.145 Angle : 0.595 6.906 7000 Z= 0.311 Chirality : 0.050 0.194 826 Planarity : 0.005 0.068 861 Dihedral : 5.034 16.852 693 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.20 % Allowed : 24.91 % Favored : 72.89 % 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 aren not related in a simple way. whole: -2.58 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 104 TYR 0.012 0.001 TYR C 114 PHE 0.007 0.001 PHE E 64 TRP 0.003 0.001 TRP C 79 HIS 0.002 0.000 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5145) covalent geometry : angle 0.59455 ( 7000) hydrogen bonds : bond 0.02088 ( 114) hydrogen bonds : angle 4.65694 ( 342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8173 (ttt) cc_final: 0.7813 (tpt) REVERT: A 92 GLU cc_start: 0.8484 (pt0) cc_final: 0.7680 (tm-30) REVERT: B 92 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: B 104 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7788 (ttm110) REVERT: C 92 GLU cc_start: 0.8587 (pt0) cc_final: 0.7759 (tm-30) REVERT: D 13 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7473 (tmt) REVERT: D 21 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7503 (mmm-85) REVERT: D 35 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8241 (ttmm) REVERT: D 92 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 13 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6836 (tmt) REVERT: E 21 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7823 (tpp80) REVERT: E 92 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7810 (tm-30) REVERT: F 13 MET cc_start: 0.7885 (tmt) cc_final: 0.7480 (tmt) REVERT: F 21 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7758 (tpp80) REVERT: F 104 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8178 (ttm110) REVERT: G 13 MET cc_start: 0.7856 (tmm) cc_final: 0.7422 (tmt) REVERT: G 80 LYS cc_start: 0.8211 (tttt) cc_final: 0.7898 (tttm) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.5940 time to fit residues: 67.1577 Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.149029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.124173 restraints weight = 5792.860| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.55 r_work: 0.3873 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5145 Z= 0.246 Angle : 0.659 6.633 7000 Z= 0.346 Chirality : 0.052 0.222 826 Planarity : 0.004 0.057 861 Dihedral : 5.251 18.836 693 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.01 % Allowed : 25.82 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 104 TYR 0.012 0.002 TYR C 114 PHE 0.007 0.002 PHE E 64 TRP 0.007 0.002 TRP E 79 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 5145) covalent geometry : angle 0.65912 ( 7000) hydrogen bonds : bond 0.02413 ( 114) hydrogen bonds : angle 4.81891 ( 342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.65 seconds wall clock time: 36 minutes 38.20 seconds (2198.20 seconds total)