Starting phenix.real_space_refine on Tue Aug 4 13:59:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.map" model { file = "/net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xmg_67024/08_2026/9xmg_67024.cif" } resolution = 3.3 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2325 2.51 5 N 590 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3595 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.73, per 1000 atoms: 0.20 Number of scatterers: 3595 At special positions: 0 Unit cell: (68.89, 86.32, 41.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 675 8.00 N 590 7.00 C 2325 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: 0.28 Conformation dependent library (CDL) restraints added in 138.4 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.161A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 22 removed outlier: 6.458A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 27 removed outlier: 6.847A pdb=" N ILE A 26 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.565A pdb=" N VAL A 30 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE B 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 32 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE E 33 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.641A pdb=" N THR C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLU D 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLU C 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL D 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N PHE C 64 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU C 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU A 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL C 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N PHE A 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 64 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 65 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU B 66 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE E 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 65 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU E 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 72 through 75 removed outlier: 8.242A pdb=" N ILE C 73 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE A 73 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 75 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.634A pdb=" N GLU A 92 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE B 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 94 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER B 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 96 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU B 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE E 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N SER E 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR B 96 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 104 through 110 removed outlier: 9.094A pdb=" N ARG C 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ILE D 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N ALA D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N ARG A 104 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N ILE C 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N ALA C 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N ALA B 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 107 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU B 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR B 105 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR E 106 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 107 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA E 108 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115 removed outlier: 7.035A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 121 removed outlier: 5.949A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR A 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 0.49 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1120 1.34 - 1.45: 541 1.45 - 1.57: 2009 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 3680 Sorted by residual: bond pdb=" CG1 ILE C 73 " pdb=" CD1 ILE C 73 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CG1 ILE D 73 " pdb=" CD1 ILE D 73 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.07e+00 bond pdb=" CG LEU C 111 " pdb=" CD1 LEU C 111 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG1 ILE A 73 " pdb=" CD1 ILE A 73 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.05e+00 bond pdb=" CG1 ILE B 73 " pdb=" CD1 ILE B 73 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 ... (remaining 3675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 4669 1.26 - 2.51: 282 2.51 - 3.77: 44 3.77 - 5.03: 5 5.03 - 6.28: 5 Bond angle restraints: 5005 Sorted by residual: angle pdb=" N SER C 85 " pdb=" CA SER C 85 " pdb=" C SER C 85 " ideal model delta sigma weight residual 109.81 113.81 -4.00 2.21e+00 2.05e-01 3.27e+00 angle pdb=" CA LEU C 12 " pdb=" CB LEU C 12 " pdb=" CG LEU C 12 " ideal model delta sigma weight residual 116.30 122.58 -6.28 3.50e+00 8.16e-02 3.22e+00 angle pdb=" CA LEU E 12 " pdb=" CB LEU E 12 " pdb=" CG LEU E 12 " ideal model delta sigma weight residual 116.30 122.56 -6.26 3.50e+00 8.16e-02 3.20e+00 angle pdb=" N SER A 85 " pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 109.81 113.76 -3.95 2.21e+00 2.05e-01 3.19e+00 angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 109.81 113.75 -3.94 2.21e+00 2.05e-01 3.18e+00 ... (remaining 5000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.06: 1640 8.06 - 16.12: 315 16.12 - 24.18: 135 24.18 - 32.24: 45 32.24 - 40.30: 35 Dihedral angle restraints: 2170 sinusoidal: 825 harmonic: 1345 Sorted by residual: dihedral pdb=" CA ALA C 25 " pdb=" C ALA C 25 " pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA B 25 " pdb=" C ALA B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual -180.00 -162.07 -17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA E 25 " pdb=" C ALA E 25 " pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 244 0.027 - 0.054: 184 0.054 - 0.081: 84 0.081 - 0.108: 65 0.108 - 0.135: 13 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE E 73 " pdb=" N ILE E 73 " pdb=" C ILE E 73 " pdb=" CB ILE E 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 587 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C SER D 100 " -0.023 2.00e-02 2.50e+03 pdb=" O SER D 100 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY D 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C SER A 100 " -0.023 2.00e-02 2.50e+03 pdb=" O SER A 100 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 100 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C SER B 100 " -0.022 2.00e-02 2.50e+03 pdb=" O SER B 100 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.008 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 321 2.74 - 3.28: 3356 3.28 - 3.82: 5688 3.82 - 4.36: 7014 4.36 - 4.90: 13734 Nonbonded interactions: 30113 Sorted by model distance: nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 119 " pdb=" OH TYR D 114 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR E 119 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR B 119 " model vdw 2.215 3.040 nonbonded pdb=" O SER A 117 " pdb=" OG SER B 117 " model vdw 2.303 3.040 ... (remaining 30108 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.120 Find NCS groups from input model: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.008 0.041 3680 Z= 0.354 Angle : 0.689 6.285 5005 Z= 0.388 Chirality : 0.051 0.135 590 Planarity : 0.004 0.023 615 Dihedral : 11.897 40.302 1300 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % 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: -4.56 (0.27), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.21), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 34 TYR 0.017 0.002 TYR B 114 PHE 0.013 0.002 PHE C 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.35 ( 3680) covalent geometry : angle 0.68943 / 0.39 ( 5005) hydrogen bonds : bond 0.15873 / 10.08 ( 54) hydrogen bonds : angle 7.97140 / 5.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.136 Fit side-chains REVERT: A 34 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7060 (tmt170) REVERT: A 70 LYS cc_start: 0.8888 (tttt) cc_final: 0.8621 (tttm) REVERT: B 70 LYS cc_start: 0.8940 (tttt) cc_final: 0.8490 (ttmt) REVERT: B 89 GLU cc_start: 0.8399 (pt0) cc_final: 0.8154 (pt0) REVERT: C 21 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7683 (ttm-80) REVERT: C 58 LEU cc_start: 0.8506 (tp) cc_final: 0.8270 (tp) REVERT: C 70 LYS cc_start: 0.8901 (tttt) cc_final: 0.8440 (tttm) REVERT: D 21 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: D 70 LYS cc_start: 0.8857 (tttt) cc_final: 0.8470 (ttmt) REVERT: E 70 LYS cc_start: 0.8921 (tttt) cc_final: 0.8614 (ttpt) REVERT: E 89 GLU cc_start: 0.8529 (pt0) cc_final: 0.8319 (pt0) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1086 time to fit residues: 8.6804 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS D 88 HIS E 88 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.124240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103449 restraints weight = 4461.337| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.42 r_work: 0.3514 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 0.018 3680 Z= 0.116 Angle : 0.535 5.315 5005 Z= 0.277 Chirality : 0.048 0.125 590 Planarity : 0.003 0.025 615 Dihedral : 4.746 17.430 495 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.29 % Allowed : 14.43 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.017 0.001 TYR C 114 PHE 0.010 0.002 PHE C 95 TRP 0.002 0.000 TRP B 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3680) covalent geometry : angle 0.53453 / 0.28 ( 5005) hydrogen bonds : bond 0.02533 / 1.40 ( 54) hydrogen bonds : angle 5.67862 / 3.85 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7730 (ttt-90) REVERT: A 34 ARG cc_start: 0.7616 (ttt90) cc_final: 0.6960 (tmt170) REVERT: A 70 LYS cc_start: 0.8911 (tttt) cc_final: 0.8706 (tttm) REVERT: B 34 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7207 (tpt90) REVERT: B 70 LYS cc_start: 0.8995 (tttt) cc_final: 0.8729 (ttpt) REVERT: C 21 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7603 (ttt-90) REVERT: C 58 LEU cc_start: 0.8511 (tp) cc_final: 0.8219 (tp) REVERT: C 70 LYS cc_start: 0.8920 (tttt) cc_final: 0.8505 (tttm) REVERT: C 80 LYS cc_start: 0.8310 (tttt) cc_final: 0.7907 (tttp) REVERT: D 21 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8408 (ttm-80) REVERT: D 70 LYS cc_start: 0.8880 (tttt) cc_final: 0.8489 (ttmt) REVERT: D 80 LYS cc_start: 0.8494 (tttt) cc_final: 0.8172 (tttp) REVERT: E 34 ARG cc_start: 0.8381 (ttt90) cc_final: 0.8164 (tpt-90) REVERT: E 70 LYS cc_start: 0.9017 (tttt) cc_final: 0.8773 (ttpt) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1154 time to fit residues: 10.3820 Evaluate side-chains 84 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096174 restraints weight = 4509.586| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.55 r_work: 0.3366 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3680 Z= 0.297 Angle : 0.625 5.227 5005 Z= 0.328 Chirality : 0.051 0.138 590 Planarity : 0.004 0.027 615 Dihedral : 5.042 19.154 495 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.57 % Allowed : 14.68 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 103 TYR 0.018 0.002 TYR C 114 PHE 0.016 0.003 PHE D 33 TRP 0.006 0.001 TRP D 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.30 ( 3680) covalent geometry : angle 0.62527 / 0.33 ( 5005) hydrogen bonds : bond 0.03524 / 2.08 ( 54) hydrogen bonds : angle 5.53793 / 3.78 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7723 (ttt90) REVERT: A 34 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7085 (tmt170) REVERT: A 70 LYS cc_start: 0.8839 (tttt) cc_final: 0.8624 (tttm) REVERT: B 34 ARG cc_start: 0.7796 (ttt90) cc_final: 0.7170 (tpt90) REVERT: B 70 LYS cc_start: 0.8940 (tttt) cc_final: 0.8534 (tttt) REVERT: C 21 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: C 70 LYS cc_start: 0.8854 (tttt) cc_final: 0.8595 (tttm) REVERT: C 80 LYS cc_start: 0.8428 (tttt) cc_final: 0.8040 (tttm) REVERT: D 21 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8343 (ttm-80) REVERT: D 70 LYS cc_start: 0.8862 (tttt) cc_final: 0.8524 (ttmt) REVERT: D 80 LYS cc_start: 0.8502 (tttt) cc_final: 0.8196 (tttp) REVERT: E 70 LYS cc_start: 0.9024 (tttt) cc_final: 0.8808 (ttpt) outliers start: 22 outliers final: 19 residues processed: 75 average time/residue: 0.0718 time to fit residues: 6.2098 Evaluate side-chains 85 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3858 r_free = 0.3858 target = 0.124544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103146 restraints weight = 4352.251| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.51 r_work: 0.3462 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3680 Z= 0.156 Angle : 0.535 4.423 5005 Z= 0.279 Chirality : 0.048 0.130 590 Planarity : 0.003 0.026 615 Dihedral : 4.715 17.748 495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.06 % Allowed : 15.44 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.018 0.002 TYR C 114 PHE 0.009 0.002 PHE C 95 TRP 0.001 0.000 TRP A 79 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 3680) covalent geometry : angle 0.53463 / 0.28 ( 5005) hydrogen bonds : bond 0.02477 / 1.41 ( 54) hydrogen bonds : angle 5.13990 / 3.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7680 (ttt90) REVERT: A 34 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7087 (tmt170) REVERT: A 70 LYS cc_start: 0.8865 (tttt) cc_final: 0.8500 (tttm) REVERT: B 34 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7123 (tmt170) REVERT: B 58 LEU cc_start: 0.8315 (tp) cc_final: 0.8093 (tp) REVERT: B 70 LYS cc_start: 0.8959 (tttt) cc_final: 0.8663 (ttpt) REVERT: C 70 LYS cc_start: 0.8855 (tttt) cc_final: 0.8545 (tttm) REVERT: C 80 LYS cc_start: 0.8341 (tttt) cc_final: 0.7983 (tttm) REVERT: D 21 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: D 70 LYS cc_start: 0.8840 (tttt) cc_final: 0.8449 (ttmt) REVERT: D 80 LYS cc_start: 0.8562 (tttt) cc_final: 0.8232 (tttp) REVERT: E 34 ARG cc_start: 0.8407 (ttt90) cc_final: 0.7772 (tmt170) outliers start: 20 outliers final: 19 residues processed: 75 average time/residue: 0.1198 time to fit residues: 10.2945 Evaluate side-chains 87 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3900 r_free = 0.3900 target = 0.127372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106202 restraints weight = 4341.293| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.50 r_work: 0.3525 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3680 Z= 0.118 Angle : 0.503 4.317 5005 Z= 0.263 Chirality : 0.047 0.127 590 Planarity : 0.003 0.024 615 Dihedral : 4.464 16.906 495 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.82 % Allowed : 14.94 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.017 0.001 TYR C 114 PHE 0.009 0.002 PHE C 95 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 3680) covalent geometry : angle 0.50345 / 0.26 ( 5005) hydrogen bonds : bond 0.02173 / 1.21 ( 54) hydrogen bonds : angle 4.94657 / 3.33 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7633 (ttt90) REVERT: A 34 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7019 (tmt170) REVERT: A 70 LYS cc_start: 0.8832 (tttt) cc_final: 0.8516 (ttpt) REVERT: B 34 ARG cc_start: 0.7729 (ttt90) cc_final: 0.7065 (tpt90) REVERT: B 70 LYS cc_start: 0.8890 (tttt) cc_final: 0.8622 (ttpt) REVERT: C 70 LYS cc_start: 0.8830 (tttt) cc_final: 0.8489 (tttm) REVERT: C 80 LYS cc_start: 0.8318 (tttt) cc_final: 0.7946 (tttm) REVERT: C 98 ASN cc_start: 0.8309 (m110) cc_final: 0.7958 (m110) REVERT: D 21 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8277 (ttm-80) REVERT: D 70 LYS cc_start: 0.8820 (tttt) cc_final: 0.8432 (ttmt) REVERT: D 80 LYS cc_start: 0.8508 (tttt) cc_final: 0.8162 (tttp) outliers start: 23 outliers final: 19 residues processed: 77 average time/residue: 0.1114 time to fit residues: 9.9031 Evaluate side-chains 86 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3883 r_free = 0.3883 target = 0.125112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103664 restraints weight = 4399.330| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.49 r_work: 0.3496 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3680 Z= 0.139 Angle : 0.512 4.266 5005 Z= 0.269 Chirality : 0.048 0.130 590 Planarity : 0.003 0.029 615 Dihedral : 4.479 16.985 495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.82 % Allowed : 15.70 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.016 0.001 TYR C 114 PHE 0.008 0.002 PHE C 95 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.000 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 3680) covalent geometry : angle 0.51249 / 0.27 ( 5005) hydrogen bonds : bond 0.02258 / 1.29 ( 54) hydrogen bonds : angle 4.93127 / 3.33 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7672 (ttt90) REVERT: A 34 ARG cc_start: 0.7697 (ttt90) cc_final: 0.7084 (tmt170) REVERT: A 70 LYS cc_start: 0.8881 (tttt) cc_final: 0.8602 (ttmt) REVERT: B 34 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7139 (tmt170) REVERT: B 70 LYS cc_start: 0.8945 (tttt) cc_final: 0.8690 (ttpt) REVERT: C 70 LYS cc_start: 0.8871 (tttt) cc_final: 0.8541 (tttm) REVERT: C 80 LYS cc_start: 0.8403 (tttt) cc_final: 0.8050 (tttm) REVERT: C 98 ASN cc_start: 0.8375 (m110) cc_final: 0.8007 (m110) REVERT: D 21 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: D 70 LYS cc_start: 0.8856 (tttt) cc_final: 0.8473 (ttmt) REVERT: D 80 LYS cc_start: 0.8585 (tttt) cc_final: 0.8246 (tttp) outliers start: 23 outliers final: 21 residues processed: 77 average time/residue: 0.0702 time to fit residues: 6.2816 Evaluate side-chains 89 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3857 r_free = 0.3857 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101923 restraints weight = 4542.644| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.57 r_work: 0.3457 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3680 Z= 0.176 Angle : 0.535 4.386 5005 Z= 0.281 Chirality : 0.048 0.131 590 Planarity : 0.003 0.031 615 Dihedral : 4.597 17.565 495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.57 % Allowed : 15.44 % Favored : 78.99 % 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 are not related in a simple way. whole: -2.89 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 103 TYR 0.016 0.002 TYR C 114 PHE 0.010 0.002 PHE D 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 3680) covalent geometry : angle 0.53508 / 0.28 ( 5005) hydrogen bonds : bond 0.02474 / 1.44 ( 54) hydrogen bonds : angle 4.97664 / 3.37 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7687 (ttt90) REVERT: A 34 ARG cc_start: 0.7684 (ttt90) cc_final: 0.7065 (tmt170) REVERT: A 70 LYS cc_start: 0.8837 (tttt) cc_final: 0.8459 (tttm) REVERT: B 34 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7090 (tmt170) REVERT: B 70 LYS cc_start: 0.8889 (tttt) cc_final: 0.8538 (ttmt) REVERT: C 70 LYS cc_start: 0.8833 (tttt) cc_final: 0.8520 (tttm) REVERT: C 80 LYS cc_start: 0.8332 (tttt) cc_final: 0.7972 (tttp) REVERT: D 21 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8391 (ttm-80) REVERT: D 70 LYS cc_start: 0.8819 (tttt) cc_final: 0.8485 (ttmt) REVERT: D 80 LYS cc_start: 0.8546 (tttt) cc_final: 0.8160 (tttp) outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.1160 time to fit residues: 9.9894 Evaluate side-chains 90 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3850 r_free = 0.3850 target = 0.123067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101509 restraints weight = 4510.343| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.54 r_work: 0.3439 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3680 Z= 0.192 Angle : 0.545 4.404 5005 Z= 0.286 Chirality : 0.049 0.131 590 Planarity : 0.003 0.032 615 Dihedral : 4.666 17.630 495 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.57 % Allowed : 14.68 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 103 TYR 0.017 0.002 TYR C 114 PHE 0.011 0.002 PHE C 33 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 ( 3680) covalent geometry : angle 0.54497 / 0.29 ( 5005) hydrogen bonds : bond 0.02573 / 1.50 ( 54) hydrogen bonds : angle 5.02332 / 3.41 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7697 (ttt90) REVERT: A 34 ARG cc_start: 0.7723 (ttt90) cc_final: 0.7130 (tmt170) REVERT: A 70 LYS cc_start: 0.8849 (tttt) cc_final: 0.8475 (tttm) REVERT: B 34 ARG cc_start: 0.7761 (ttt90) cc_final: 0.7109 (tmt170) REVERT: B 70 LYS cc_start: 0.8928 (tttt) cc_final: 0.8490 (tttt) REVERT: C 70 LYS cc_start: 0.8845 (tttt) cc_final: 0.8537 (tttm) REVERT: C 80 LYS cc_start: 0.8354 (tttt) cc_final: 0.7987 (tttm) REVERT: D 70 LYS cc_start: 0.8835 (tttt) cc_final: 0.8493 (ttmt) REVERT: D 80 LYS cc_start: 0.8563 (tttt) cc_final: 0.8175 (tttp) outliers start: 22 outliers final: 22 residues processed: 75 average time/residue: 0.1097 time to fit residues: 9.5239 Evaluate side-chains 91 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3812 r_free = 0.3812 target = 0.119586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098124 restraints weight = 4487.041| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.48 r_work: 0.3434 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3680 Z= 0.241 Angle : 0.579 4.545 5005 Z= 0.304 Chirality : 0.049 0.133 590 Planarity : 0.004 0.030 615 Dihedral : 4.806 18.701 495 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.57 % Allowed : 15.19 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 103 TYR 0.016 0.002 TYR C 114 PHE 0.014 0.002 PHE E 33 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 ( 3680) covalent geometry : angle 0.57916 / 0.30 ( 5005) hydrogen bonds : bond 0.02840 / 1.66 ( 54) hydrogen bonds : angle 5.10877 / 3.47 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7763 (ttt90) REVERT: A 34 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7142 (tmt170) REVERT: A 70 LYS cc_start: 0.8847 (tttt) cc_final: 0.8471 (tttm) REVERT: B 34 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7090 (tmt170) REVERT: B 70 LYS cc_start: 0.8955 (tttt) cc_final: 0.8525 (tttt) REVERT: C 70 LYS cc_start: 0.8875 (tttt) cc_final: 0.8589 (tttm) REVERT: C 80 LYS cc_start: 0.8463 (tttt) cc_final: 0.8103 (tttp) REVERT: D 70 LYS cc_start: 0.8865 (tttt) cc_final: 0.8529 (ttmt) REVERT: D 80 LYS cc_start: 0.8594 (tttt) cc_final: 0.8236 (tttp) outliers start: 22 outliers final: 21 residues processed: 76 average time/residue: 0.1011 time to fit residues: 8.8642 Evaluate side-chains 90 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3857 r_free = 0.3857 target = 0.122810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101449 restraints weight = 4540.476| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.50 r_work: 0.3474 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3680 Z= 0.163 Angle : 0.532 4.643 5005 Z= 0.278 Chirality : 0.048 0.130 590 Planarity : 0.003 0.034 615 Dihedral : 4.630 17.483 495 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.06 % Allowed : 15.95 % Favored : 78.99 % 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 are not related in a simple way. whole: -2.85 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.017 0.001 TYR C 114 PHE 0.010 0.002 PHE C 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 3680) covalent geometry : angle 0.53170 / 0.28 ( 5005) hydrogen bonds : bond 0.02386 / 1.37 ( 54) hydrogen bonds : angle 4.97320 / 3.36 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7693 (ttt90) REVERT: A 34 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7074 (tmt170) REVERT: A 70 LYS cc_start: 0.8877 (tttt) cc_final: 0.8589 (ttmt) REVERT: B 34 ARG cc_start: 0.7813 (ttt90) cc_final: 0.7167 (tmt170) REVERT: B 70 LYS cc_start: 0.8951 (tttt) cc_final: 0.8522 (tttt) REVERT: C 58 LEU cc_start: 0.8562 (tp) cc_final: 0.8273 (tp) REVERT: C 70 LYS cc_start: 0.8849 (tttt) cc_final: 0.8544 (tttm) REVERT: C 80 LYS cc_start: 0.8395 (tttt) cc_final: 0.8019 (tttm) REVERT: C 98 ASN cc_start: 0.8367 (m110) cc_final: 0.7981 (m110) REVERT: D 21 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8336 (ttm-80) REVERT: D 70 LYS cc_start: 0.8857 (tttt) cc_final: 0.8474 (ttmt) REVERT: D 80 LYS cc_start: 0.8583 (tttt) cc_final: 0.8206 (tttp) outliers start: 20 outliers final: 20 residues processed: 76 average time/residue: 0.1124 time to fit residues: 9.8023 Evaluate side-chains 90 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3916 r_free = 0.3916 target = 0.127204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106257 restraints weight = 4351.194| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.45 r_work: 0.3543 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3680 Z= 0.107 Angle : 0.494 4.385 5005 Z= 0.259 Chirality : 0.047 0.127 590 Planarity : 0.003 0.038 615 Dihedral : 4.376 16.406 495 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.06 % Allowed : 15.95 % Favored : 78.99 % 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 are not related in a simple way. whole: -2.77 (0.34), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.016 0.001 TYR C 114 PHE 0.009 0.001 PHE C 95 TRP 0.002 0.001 TRP C 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 3680) covalent geometry : angle 0.49426 / 0.26 ( 5005) hydrogen bonds : bond 0.02001 / 1.09 ( 54) hydrogen bonds : angle 4.82637 / 3.25 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1037.52 seconds wall clock time: 18 minutes 27.17 seconds (1107.17 seconds total)