Starting phenix.real_space_refine on Tue Feb 11 07:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc0_36149/02_2025/8jc0_36149.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.073 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 37 5.16 5 C 3048 2.51 5 N 741 2.21 5 O 865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4691 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.48, per 1000 atoms: 0.74 Number of scatterers: 4691 At special positions: 0 Unit cell: (69.568, 91.308, 105.439, 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 37 16.00 O 865 8.00 N 741 7.00 C 3048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.04 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 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: 1.07 Conformation dependent library (CDL) restraints added in 509.3 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1098 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 10 sheets defined 39.7% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'a' and resid 31 through 56 removed outlier: 3.949A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 52 removed outlier: 4.047A pdb=" N CYS b 32 " --> pdb=" O ASP b 28 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR b 33 " --> pdb=" O PRO b 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU b 34 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY b 37 " --> pdb=" O TYR b 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 126 removed outlier: 4.464A pdb=" N THR d 110 " --> pdb=" O GLY d 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE d 113 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 4.083A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 151 removed outlier: 4.199A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR e 150 " --> pdb=" O LEU e 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 Processing helix chain 'f' and resid 132 through 154 removed outlier: 3.951A pdb=" N LEU f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 113 through 140 removed outlier: 3.799A pdb=" N VAL g 124 " --> pdb=" O PHE g 120 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE g 126 " --> pdb=" O GLU g 122 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE g 135 " --> pdb=" O VAL g 131 " (cutoff:3.500A) Processing helix chain 'm' and resid 258 through 289 removed outlier: 3.892A pdb=" N ALA m 278 " --> pdb=" O ALA m 274 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 269 removed outlier: 3.762A pdb=" N LEU n 257 " --> pdb=" O LEU n 253 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR n 260 " --> pdb=" O GLN n 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR n 264 " --> pdb=" O THR n 260 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET n 265 " --> pdb=" O SER n 261 " (cutoff:3.500A) Processing helix chain 'n' and resid 269 through 286 removed outlier: 3.685A pdb=" N SER n 273 " --> pdb=" O LEU n 269 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL n 274 " --> pdb=" O LEU n 270 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL n 275 " --> pdb=" O LEU n 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG n 286 " --> pdb=" O CYS n 282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 36 removed outlier: 6.449A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 5.218A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 38 through 41 removed outlier: 3.501A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 57 through 59 removed outlier: 3.676A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.712A pdb=" N GLY f 76 " --> pdb=" O SER f 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 65 through 66 removed outlier: 3.707A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR f 99 " --> pdb=" O LEU f 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN f 60 " --> pdb=" O VAL f 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL f 97 " --> pdb=" O GLN f 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 111 through 114 removed outlier: 6.473A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR g 85 " --> pdb=" O LEU g 97 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN g 86 " --> pdb=" O PHE g 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 122 through 123 removed outlier: 3.577A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.722A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU g 74 " --> pdb=" O VAL g 42 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 597 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: 1.19 Time building geometry restraints manager: 1.28 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: 1449 1.34 - 1.47: 1131 1.47 - 1.59: 2148 1.59 - 1.71: 2 1.71 - 1.83: 51 Bond restraints: 4781 Sorted by residual: bond pdb=" CB PRO f 50 " pdb=" CG PRO f 50 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.27e+00 bond pdb=" CB PRO f 35 " pdb=" CG PRO f 35 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.85e+00 bond pdb=" CA ASP f 80 " pdb=" CB ASP f 80 " ideal model delta sigma weight residual 1.533 1.560 -0.026 2.15e-02 2.16e+03 1.49e+00 bond pdb=" N VAL d 33 " pdb=" CA VAL d 33 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.24e-02 6.50e+03 1.35e+00 bond pdb=" CA ASP d 66 " pdb=" CB ASP d 66 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.31e+00 ... (remaining 4776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 6425 2.54 - 5.08: 43 5.08 - 7.61: 9 7.61 - 10.15: 1 10.15 - 12.69: 2 Bond angle restraints: 6480 Sorted by residual: angle pdb=" CA PRO f 50 " pdb=" N PRO f 50 " pdb=" CD PRO f 50 " ideal model delta sigma weight residual 112.00 106.32 5.68 1.40e+00 5.10e-01 1.65e+01 angle pdb=" CA PRO f 35 " pdb=" N PRO f 35 " pdb=" CD PRO f 35 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA LEU d 29 " pdb=" CB LEU d 29 " pdb=" CG LEU d 29 " ideal model delta sigma weight residual 116.30 128.99 -12.69 3.50e+00 8.16e-02 1.31e+01 angle pdb=" CB MET f 128 " pdb=" CG MET f 128 " pdb=" SD MET f 128 " ideal model delta sigma weight residual 112.70 123.48 -10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET f 128 " pdb=" CB MET f 128 " pdb=" CG MET f 128 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 ... (remaining 6475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2531 17.94 - 35.89: 300 35.89 - 53.83: 65 53.83 - 71.77: 11 71.77 - 89.71: 7 Dihedral angle restraints: 2914 sinusoidal: 1201 harmonic: 1713 Sorted by residual: dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual -86.00 -165.61 79.61 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual 93.00 157.36 -64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -142.71 56.71 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 2911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 471 0.030 - 0.059: 200 0.059 - 0.089: 58 0.089 - 0.119: 26 0.119 - 0.148: 6 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA ASP f 80 " pdb=" N ASP f 80 " pdb=" C ASP f 80 " pdb=" CB ASP f 80 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ASN f 121 " pdb=" N ASN f 121 " pdb=" C ASN f 121 " pdb=" CB ASN f 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE d 70 " pdb=" N ILE d 70 " pdb=" C ILE d 70 " pdb=" CB ILE d 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 758 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS f 49 " -0.037 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO f 50 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO f 50 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO f 50 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR f 34 " 0.029 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO f 35 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO f 35 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO f 35 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP d 100 " 0.026 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO d 101 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO d 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO d 101 " 0.022 5.00e-02 4.00e+02 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 773 2.77 - 3.30: 4375 3.30 - 3.83: 7211 3.83 - 4.37: 7945 4.37 - 4.90: 14200 Nonbonded interactions: 34504 Sorted by model distance: nonbonded pdb=" O CYS d 93 " pdb=" NH1 ARG e 117 " model vdw 2.236 3.120 nonbonded pdb=" OH TYR a 42 " pdb=" OG1 THR b 47 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP b 36 " pdb=" OH TYR n 266 " model vdw 2.293 3.040 nonbonded pdb=" O ARG g 82 " pdb=" OH TYR g 85 " model vdw 2.295 3.040 nonbonded pdb=" O ALA f 108 " pdb=" NZ LYS g 95 " model vdw 2.312 3.120 ... (remaining 34499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 27 through 54) selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 4781 Z= 0.236 Angle : 0.652 12.690 6480 Z= 0.369 Chirality : 0.039 0.148 761 Planarity : 0.004 0.054 793 Dihedral : 15.868 89.715 1789 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 21.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.35), residues: 571 helix: 0.88 (0.37), residues: 213 sheet: -2.09 (0.47), residues: 117 loop : -2.57 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.006 0.001 PHE m 281 TYR 0.009 0.001 TYR d 71 ARG 0.003 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.488 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1777 time to fit residues: 13.5039 Evaluate side-chains 59 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 51 GLN e 81 HIS f 61 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.228468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183043 restraints weight = 4391.240| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.25 r_work: 0.3946 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4781 Z= 0.202 Angle : 0.566 9.262 6480 Z= 0.291 Chirality : 0.040 0.148 761 Planarity : 0.003 0.032 793 Dihedral : 4.689 37.328 699 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.49 % Allowed : 18.55 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.35), residues: 571 helix: 1.31 (0.36), residues: 215 sheet: -2.14 (0.47), residues: 117 loop : -2.57 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.007 0.001 PHE e 87 TYR 0.013 0.001 TYR n 263 ARG 0.003 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.499 Fit side-chains REVERT: a 30 LYS cc_start: 0.7236 (ptpt) cc_final: 0.6054 (tptp) REVERT: d 58 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6447 (tt) REVERT: f 128 MET cc_start: 0.5471 (tpp) cc_final: 0.5200 (tpp) REVERT: g 56 PHE cc_start: 0.7063 (m-10) cc_final: 0.6816 (m-10) REVERT: g 71 LYS cc_start: 0.7433 (mttt) cc_final: 0.7085 (mttt) REVERT: g 95 LYS cc_start: 0.8231 (ttmt) cc_final: 0.8016 (tttt) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.1666 time to fit residues: 14.8365 Evaluate side-chains 64 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 71 TYR Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.229381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.184110 restraints weight = 4451.145| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.23 r_work: 0.3948 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4781 Z= 0.162 Angle : 0.517 7.052 6480 Z= 0.268 Chirality : 0.039 0.143 761 Planarity : 0.003 0.028 793 Dihedral : 4.617 41.004 699 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.68 % Allowed : 18.55 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.36), residues: 571 helix: 1.62 (0.37), residues: 216 sheet: -2.08 (0.46), residues: 120 loop : -2.51 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 43 HIS 0.003 0.001 HIS f 81 PHE 0.005 0.001 PHE e 87 TYR 0.009 0.001 TYR n 263 ARG 0.002 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.567 Fit side-chains REVERT: a 30 LYS cc_start: 0.6966 (ptpt) cc_final: 0.5824 (tptp) REVERT: f 128 MET cc_start: 0.5648 (tpp) cc_final: 0.5257 (tpp) REVERT: g 71 LYS cc_start: 0.7466 (mttt) cc_final: 0.7081 (mttt) REVERT: g 95 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7984 (tttt) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.1706 time to fit residues: 14.3277 Evaluate side-chains 62 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.0010 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.225453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179214 restraints weight = 4489.424| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.30 r_work: 0.3895 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4781 Z= 0.214 Angle : 0.563 9.306 6480 Z= 0.284 Chirality : 0.041 0.147 761 Planarity : 0.003 0.026 793 Dihedral : 4.842 46.818 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.02 % Allowed : 17.78 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.36), residues: 571 helix: 1.55 (0.37), residues: 216 sheet: -1.95 (0.47), residues: 120 loop : -2.49 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.002 0.001 HIS f 81 PHE 0.008 0.001 PHE b 50 TYR 0.015 0.001 TYR n 263 ARG 0.001 0.000 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.542 Fit side-chains REVERT: a 30 LYS cc_start: 0.6999 (ptpt) cc_final: 0.5902 (tptp) REVERT: f 128 MET cc_start: 0.5977 (tpp) cc_final: 0.5366 (tpp) REVERT: g 71 LYS cc_start: 0.7471 (mttt) cc_final: 0.7086 (mttt) REVERT: g 84 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7443 (ttt) REVERT: g 95 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8007 (ttmt) outliers start: 21 outliers final: 14 residues processed: 70 average time/residue: 0.1478 time to fit residues: 13.7434 Evaluate side-chains 68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.225426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179132 restraints weight = 4527.522| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.30 r_work: 0.3893 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4781 Z= 0.199 Angle : 0.547 7.326 6480 Z= 0.277 Chirality : 0.040 0.149 761 Planarity : 0.002 0.024 793 Dihedral : 4.887 49.846 699 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.25 % Allowed : 19.50 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.36), residues: 571 helix: 1.58 (0.37), residues: 214 sheet: -1.75 (0.48), residues: 115 loop : -2.45 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 43 HIS 0.001 0.001 HIS d 89 PHE 0.008 0.001 PHE g 56 TYR 0.013 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.473 Fit side-chains REVERT: a 30 LYS cc_start: 0.6950 (ptpt) cc_final: 0.5881 (tptp) REVERT: a 45 ILE cc_start: 0.8333 (mt) cc_final: 0.8112 (mp) REVERT: f 128 MET cc_start: 0.6126 (tpp) cc_final: 0.5449 (tpp) REVERT: g 71 LYS cc_start: 0.7471 (mttt) cc_final: 0.7074 (mttt) REVERT: g 95 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8150 (ttmt) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.1572 time to fit residues: 13.3232 Evaluate side-chains 64 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.226001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180471 restraints weight = 4500.360| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.15 r_work: 0.3864 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4781 Z= 0.181 Angle : 0.532 6.669 6480 Z= 0.269 Chirality : 0.040 0.150 761 Planarity : 0.002 0.023 793 Dihedral : 4.857 51.765 699 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.25 % Allowed : 21.03 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.36), residues: 571 helix: 1.70 (0.36), residues: 214 sheet: -1.59 (0.48), residues: 115 loop : -2.35 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.007 0.001 PHE m 288 TYR 0.012 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.513 Fit side-chains REVERT: a 30 LYS cc_start: 0.6975 (ptpt) cc_final: 0.5958 (tptp) REVERT: e 123 MET cc_start: 0.7263 (ptp) cc_final: 0.6797 (ptm) REVERT: f 128 MET cc_start: 0.6169 (tpp) cc_final: 0.5460 (tpp) REVERT: g 71 LYS cc_start: 0.7577 (mttt) cc_final: 0.7186 (mttt) REVERT: g 95 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7935 (ttmt) outliers start: 17 outliers final: 13 residues processed: 65 average time/residue: 0.1546 time to fit residues: 13.3610 Evaluate side-chains 65 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.222239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176581 restraints weight = 4477.222| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.13 r_work: 0.3839 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4781 Z= 0.249 Angle : 0.573 6.009 6480 Z= 0.289 Chirality : 0.041 0.151 761 Planarity : 0.003 0.023 793 Dihedral : 5.065 55.155 699 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.02 % Allowed : 21.22 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.36), residues: 571 helix: 1.50 (0.36), residues: 214 sheet: -1.59 (0.48), residues: 115 loop : -2.38 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 43 HIS 0.002 0.001 HIS d 89 PHE 0.011 0.001 PHE b 50 TYR 0.017 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.664 Fit side-chains REVERT: a 30 LYS cc_start: 0.6855 (ptpt) cc_final: 0.6016 (tptp) REVERT: a 45 ILE cc_start: 0.8483 (mt) cc_final: 0.8207 (mp) REVERT: e 123 MET cc_start: 0.7301 (ptp) cc_final: 0.6846 (ptm) REVERT: f 128 MET cc_start: 0.6411 (tpp) cc_final: 0.5558 (tpp) REVERT: g 71 LYS cc_start: 0.7639 (mttt) cc_final: 0.7291 (mttt) REVERT: g 95 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7930 (ttmt) outliers start: 21 outliers final: 17 residues processed: 67 average time/residue: 0.1547 time to fit residues: 13.8756 Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.0070 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.227167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184734 restraints weight = 4417.854| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.04 r_work: 0.3918 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4781 Z= 0.152 Angle : 0.502 5.430 6480 Z= 0.260 Chirality : 0.039 0.142 761 Planarity : 0.002 0.026 793 Dihedral : 4.837 54.766 699 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.25 % Allowed : 21.99 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.36), residues: 571 helix: 1.86 (0.36), residues: 213 sheet: -1.50 (0.49), residues: 109 loop : -2.32 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.007 0.001 PHE f 87 TYR 0.009 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.501 Fit side-chains REVERT: a 30 LYS cc_start: 0.6806 (ptpt) cc_final: 0.5986 (tptp) REVERT: f 128 MET cc_start: 0.6151 (tpp) cc_final: 0.5400 (tpp) REVERT: g 56 PHE cc_start: 0.6915 (m-10) cc_final: 0.6591 (m-10) REVERT: g 71 LYS cc_start: 0.7541 (mttt) cc_final: 0.7164 (mttt) REVERT: g 95 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7867 (ttmt) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.1633 time to fit residues: 14.2577 Evaluate side-chains 66 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.225469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178931 restraints weight = 4459.353| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.29 r_work: 0.3858 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4781 Z= 0.188 Angle : 0.529 6.240 6480 Z= 0.271 Chirality : 0.040 0.144 761 Planarity : 0.002 0.025 793 Dihedral : 4.858 55.871 699 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.63 % Allowed : 21.99 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.36), residues: 571 helix: 1.77 (0.36), residues: 214 sheet: -1.38 (0.49), residues: 109 loop : -2.37 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.008 0.001 PHE m 288 TYR 0.012 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.469 Fit side-chains REVERT: a 30 LYS cc_start: 0.6788 (ptpt) cc_final: 0.5971 (tptp) REVERT: e 123 MET cc_start: 0.7169 (ptp) cc_final: 0.6724 (ptm) REVERT: f 128 MET cc_start: 0.6314 (tpp) cc_final: 0.5466 (tpp) REVERT: g 56 PHE cc_start: 0.7049 (m-10) cc_final: 0.6717 (m-10) REVERT: g 71 LYS cc_start: 0.7551 (mttt) cc_final: 0.7165 (mttt) REVERT: g 95 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7889 (ttmt) REVERT: g 105 GLN cc_start: 0.5472 (OUTLIER) cc_final: 0.5238 (pt0) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.1598 time to fit residues: 13.9190 Evaluate side-chains 68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.226601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180320 restraints weight = 4399.018| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.26 r_work: 0.3897 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4781 Z= 0.171 Angle : 0.516 5.690 6480 Z= 0.266 Chirality : 0.040 0.143 761 Planarity : 0.002 0.026 793 Dihedral : 4.798 56.351 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.44 % Allowed : 22.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.36), residues: 571 helix: 1.83 (0.36), residues: 214 sheet: -1.21 (0.50), residues: 109 loop : -2.35 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.007 0.001 PHE m 288 TYR 0.011 0.001 TYR n 263 ARG 0.001 0.000 ARG d 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.618 Fit side-chains REVERT: a 30 LYS cc_start: 0.6771 (ptpt) cc_final: 0.5972 (tptp) REVERT: e 123 MET cc_start: 0.7245 (ptp) cc_final: 0.6793 (ptm) REVERT: f 128 MET cc_start: 0.6297 (tpp) cc_final: 0.5489 (tpp) REVERT: g 56 PHE cc_start: 0.6983 (m-10) cc_final: 0.6684 (m-10) REVERT: g 71 LYS cc_start: 0.7581 (mttt) cc_final: 0.7202 (mttt) REVERT: g 95 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7870 (tttt) REVERT: g 105 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.5070 (pp30) outliers start: 18 outliers final: 15 residues processed: 62 average time/residue: 0.1674 time to fit residues: 13.7492 Evaluate side-chains 65 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 68 ARG Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.223392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177575 restraints weight = 4494.640| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.11 r_work: 0.3845 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4781 Z= 0.228 Angle : 0.553 5.479 6480 Z= 0.282 Chirality : 0.041 0.148 761 Planarity : 0.003 0.024 793 Dihedral : 5.019 59.211 699 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.06 % Allowed : 22.56 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.36), residues: 571 helix: 1.66 (0.36), residues: 214 sheet: -1.22 (0.51), residues: 109 loop : -2.38 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.002 0.001 HIS d 89 PHE 0.009 0.001 PHE b 50 TYR 0.016 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.34 seconds wall clock time: 52 minutes 16.54 seconds (3136.54 seconds total)