Starting phenix.real_space_refine on Sat May 10 02:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc0_36149/05_2025/8jc0_36149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc0_36149/05_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_36149/05_2025/8jc0_36149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc0_36149/05_2025/8jc0_36149.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc0_36149/05_2025/8jc0_36149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc0_36149/05_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-5687/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: 3.38, per 1000 atoms: 0.72 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: 1.22 Conformation dependent library (CDL) restraints added in 511.9 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: 0.49 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: 1.09 Time building geometry restraints manager: 1.40 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: 0.330 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.120 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 4790 Z= 0.143 Angle : 0.655 12.690 6498 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 Details of bonding type rmsd hydrogen bonds : bond 0.20981 ( 212) hydrogen bonds : angle 6.78326 ( 597) SS BOND : bond 0.00223 ( 9) SS BOND : angle 1.25126 ( 18) covalent geometry : bond 0.00343 ( 4781) covalent geometry : angle 0.65216 ( 6480) *********************** 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 : 0.505 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1769 time to fit residues: 13.4481 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 : 0.549 ------------------------------------------------------------------------------- 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: 0.2980 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: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.229245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183692 restraints weight = 4387.712| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.27 r_work: 0.3948 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4790 Z= 0.123 Angle : 0.564 9.192 6498 Z= 0.290 Chirality : 0.040 0.144 761 Planarity : 0.003 0.032 793 Dihedral : 4.649 36.999 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.10 % Allowed : 18.74 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.35), residues: 571 helix: 1.36 (0.36), residues: 215 sheet: -2.20 (0.47), residues: 107 loop : -2.56 (0.35), residues: 249 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 0.006 0.001 PHE f 110 TYR 0.012 0.001 TYR n 263 ARG 0.003 0.000 ARG d 68 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 212) hydrogen bonds : angle 4.32801 ( 597) SS BOND : bond 0.00251 ( 9) SS BOND : angle 1.03852 ( 18) covalent geometry : bond 0.00288 ( 4781) covalent geometry : angle 0.56192 ( 6480) *********************** 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 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.537 Fit side-chains REVERT: a 30 LYS cc_start: 0.7242 (ptpt) cc_final: 0.6065 (tptp) REVERT: d 58 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6463 (tt) REVERT: f 128 MET cc_start: 0.5461 (tpp) cc_final: 0.5194 (tpp) REVERT: g 56 PHE cc_start: 0.7044 (m-10) cc_final: 0.6800 (m-10) REVERT: g 71 LYS cc_start: 0.7464 (mttt) cc_final: 0.7114 (mttt) REVERT: g 95 LYS cc_start: 0.8240 (ttmt) cc_final: 0.8028 (tttt) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1720 time to fit residues: 14.7017 Evaluate side-chains 60 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain d residue 58 LEU 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: 0.8980 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.229827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.188981 restraints weight = 4444.973| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.97 r_work: 0.3953 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4790 Z= 0.105 Angle : 0.520 7.248 6498 Z= 0.269 Chirality : 0.039 0.144 761 Planarity : 0.003 0.028 793 Dihedral : 4.577 40.115 699 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.56 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: -1.20 (0.36), residues: 571 helix: 1.65 (0.37), residues: 216 sheet: -2.06 (0.46), residues: 120 loop : -2.50 (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 m 288 TYR 0.009 0.001 TYR n 263 ARG 0.002 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 212) hydrogen bonds : angle 4.00292 ( 597) SS BOND : bond 0.00335 ( 9) SS BOND : angle 0.95543 ( 18) covalent geometry : bond 0.00239 ( 4781) covalent geometry : angle 0.51872 ( 6480) *********************** 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 68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: a 30 LYS cc_start: 0.6965 (ptpt) cc_final: 0.5840 (tptp) REVERT: f 128 MET cc_start: 0.5588 (tpp) cc_final: 0.5234 (tpp) REVERT: g 71 LYS cc_start: 0.7493 (mttt) cc_final: 0.7107 (mttt) REVERT: g 95 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7974 (tttt) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.1771 time to fit residues: 14.7133 Evaluate side-chains 64 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 98 CYS 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: 4.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 36 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.225414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179535 restraints weight = 4480.852| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.27 r_work: 0.3901 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4790 Z= 0.139 Angle : 0.581 9.943 6498 Z= 0.290 Chirality : 0.041 0.150 761 Planarity : 0.003 0.026 793 Dihedral : 4.830 46.432 699 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.02 % Allowed : 17.97 % Favored : 78.01 % 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: -1.24 (0.36), residues: 571 helix: 1.51 (0.37), residues: 216 sheet: -1.92 (0.47), residues: 120 loop : -2.51 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 43 HIS 0.002 0.001 HIS f 81 PHE 0.009 0.001 PHE m 281 TYR 0.015 0.001 TYR n 263 ARG 0.002 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 212) hydrogen bonds : angle 3.88941 ( 597) SS BOND : bond 0.00215 ( 9) SS BOND : angle 1.03317 ( 18) covalent geometry : bond 0.00330 ( 4781) covalent geometry : angle 0.57962 ( 6480) *********************** 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 : 0.557 Fit side-chains REVERT: a 30 LYS cc_start: 0.7011 (ptpt) cc_final: 0.5920 (tptp) REVERT: f 128 MET cc_start: 0.5968 (tpp) cc_final: 0.5365 (tpp) REVERT: g 71 LYS cc_start: 0.7493 (mttt) cc_final: 0.7070 (mttt) REVERT: g 95 LYS cc_start: 0.8250 (mtmt) cc_final: 0.8018 (ttmt) outliers start: 21 outliers final: 14 residues processed: 70 average time/residue: 0.1483 time to fit residues: 13.8386 Evaluate side-chains 67 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.226896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180801 restraints weight = 4521.732| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.30 r_work: 0.3905 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4790 Z= 0.114 Angle : 0.534 7.572 6498 Z= 0.271 Chirality : 0.040 0.149 761 Planarity : 0.002 0.024 793 Dihedral : 4.798 48.575 699 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.63 % Allowed : 18.74 % Favored : 77.63 % 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: -1.04 (0.36), residues: 571 helix: 1.67 (0.37), residues: 214 sheet: -1.76 (0.47), residues: 120 loop : -2.39 (0.37), residues: 237 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 0.006 0.001 PHE m 288 TYR 0.011 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 212) hydrogen bonds : angle 3.72970 ( 597) SS BOND : bond 0.00220 ( 9) SS BOND : angle 1.14697 ( 18) covalent geometry : bond 0.00266 ( 4781) covalent geometry : angle 0.53163 ( 6480) *********************** 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 73 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.496 Fit side-chains REVERT: a 30 LYS cc_start: 0.6976 (ptpt) cc_final: 0.5869 (tptp) REVERT: a 45 ILE cc_start: 0.8336 (mt) cc_final: 0.8126 (mp) REVERT: f 128 MET cc_start: 0.6021 (tpp) cc_final: 0.5379 (tpp) REVERT: g 56 PHE cc_start: 0.6949 (m-10) cc_final: 0.6651 (m-10) REVERT: g 71 LYS cc_start: 0.7429 (mttt) cc_final: 0.7026 (mttt) REVERT: g 95 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7884 (ttmt) REVERT: m 271 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7440 (tpp) outliers start: 19 outliers final: 14 residues processed: 67 average time/residue: 0.1497 time to fit residues: 13.3817 Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 m residue 271 MET 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: 0.0010 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.229013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.184538 restraints weight = 4497.285| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.17 r_work: 0.3901 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4790 Z= 0.097 Angle : 0.507 6.974 6498 Z= 0.258 Chirality : 0.039 0.145 761 Planarity : 0.002 0.023 793 Dihedral : 4.636 49.297 699 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.63 % Allowed : 19.89 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.36), residues: 571 helix: 1.88 (0.37), residues: 214 sheet: -1.49 (0.49), residues: 115 loop : -2.34 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.006 0.001 PHE f 87 TYR 0.008 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 212) hydrogen bonds : angle 3.48648 ( 597) SS BOND : bond 0.00197 ( 9) SS BOND : angle 1.02299 ( 18) covalent geometry : bond 0.00220 ( 4781) covalent geometry : angle 0.50448 ( 6480) *********************** 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 71 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.486 Fit side-chains REVERT: a 30 LYS cc_start: 0.6930 (ptpt) cc_final: 0.5928 (tptp) REVERT: a 45 ILE cc_start: 0.8316 (mt) cc_final: 0.8077 (mp) REVERT: f 128 MET cc_start: 0.6019 (tpp) cc_final: 0.5463 (tpp) REVERT: g 56 PHE cc_start: 0.6976 (m-10) cc_final: 0.6685 (m-10) REVERT: g 71 LYS cc_start: 0.7546 (mttt) cc_final: 0.7164 (mttt) REVERT: g 95 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7942 (ttmt) REVERT: m 271 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7559 (tpp) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.1454 time to fit residues: 12.7775 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 : 0.482 ------------------------------------------------------------------------------- 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 71 TYR 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 m residue 271 MET 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: 0.3980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.223988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177219 restraints weight = 4477.948| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.28 r_work: 0.3858 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4790 Z= 0.146 Angle : 0.566 6.754 6498 Z= 0.285 Chirality : 0.041 0.151 761 Planarity : 0.003 0.021 793 Dihedral : 4.912 53.385 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.82 % Allowed : 20.65 % Favored : 75.53 % 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: -0.94 (0.36), residues: 571 helix: 1.64 (0.36), residues: 214 sheet: -1.49 (0.49), residues: 115 loop : -2.35 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 43 HIS 0.002 0.001 HIS d 89 PHE 0.010 0.001 PHE b 50 TYR 0.017 0.001 TYR n 263 ARG 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 212) hydrogen bonds : angle 3.68202 ( 597) SS BOND : bond 0.00210 ( 9) SS BOND : angle 1.08774 ( 18) covalent geometry : bond 0.00349 ( 4781) covalent geometry : angle 0.56435 ( 6480) *********************** 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 72 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.492 Fit side-chains REVERT: a 30 LYS cc_start: 0.6890 (ptpt) cc_final: 0.6031 (tptp) REVERT: e 123 MET cc_start: 0.7259 (ptp) cc_final: 0.6815 (ptm) REVERT: f 128 MET cc_start: 0.6019 (tpp) cc_final: 0.5359 (tpp) REVERT: g 56 PHE cc_start: 0.7007 (m-10) cc_final: 0.6742 (m-10) REVERT: g 71 LYS cc_start: 0.7595 (mttt) cc_final: 0.7234 (mttt) REVERT: g 95 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7935 (ttmt) REVERT: m 257 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7901 (mt-10) outliers start: 20 outliers final: 14 residues processed: 66 average time/residue: 0.1428 time to fit residues: 12.6058 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 : 0.485 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.0000 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.227857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182656 restraints weight = 4410.540| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.13 r_work: 0.3877 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4790 Z= 0.103 Angle : 0.521 8.413 6498 Z= 0.267 Chirality : 0.039 0.145 761 Planarity : 0.002 0.024 793 Dihedral : 4.774 53.957 699 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 : 3.06 % Allowed : 22.18 % 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: -0.77 (0.36), residues: 571 helix: 1.86 (0.36), residues: 214 sheet: -1.44 (0.49), residues: 115 loop : -2.30 (0.36), residues: 242 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 0.009 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 212) hydrogen bonds : angle 3.52322 ( 597) SS BOND : bond 0.00215 ( 9) SS BOND : angle 1.03530 ( 18) covalent geometry : bond 0.00237 ( 4781) covalent geometry : angle 0.51923 ( 6480) *********************** 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 68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.498 Fit side-chains REVERT: a 30 LYS cc_start: 0.6814 (ptpt) cc_final: 0.5978 (tptp) REVERT: e 123 MET cc_start: 0.7222 (ptp) cc_final: 0.6772 (ptm) REVERT: f 128 MET cc_start: 0.6013 (tpp) cc_final: 0.5373 (tpp) REVERT: g 56 PHE cc_start: 0.6916 (m-10) cc_final: 0.6660 (m-10) REVERT: g 71 LYS cc_start: 0.7568 (mttt) cc_final: 0.7175 (mttt) REVERT: g 95 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7860 (tttt) outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.1534 time to fit residues: 13.1662 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 : 0.491 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.226552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181028 restraints weight = 4458.448| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.10 r_work: 0.3882 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4790 Z= 0.110 Angle : 0.510 5.593 6498 Z= 0.262 Chirality : 0.040 0.144 761 Planarity : 0.002 0.023 793 Dihedral : 4.758 55.222 699 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.44 % Allowed : 21.61 % Favored : 74.95 % 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: -0.67 (0.36), residues: 571 helix: 1.93 (0.36), residues: 214 sheet: -1.32 (0.49), residues: 115 loop : -2.27 (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 f 61 PHE 0.007 0.001 PHE m 288 TYR 0.012 0.001 TYR n 263 ARG 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 212) hydrogen bonds : angle 3.48159 ( 597) SS BOND : bond 0.00210 ( 9) SS BOND : angle 0.96999 ( 18) covalent geometry : bond 0.00256 ( 4781) covalent geometry : angle 0.50861 ( 6480) *********************** 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 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.548 Fit side-chains REVERT: a 30 LYS cc_start: 0.6807 (ptpt) cc_final: 0.5976 (tptp) REVERT: e 123 MET cc_start: 0.7253 (ptp) cc_final: 0.6796 (ptm) REVERT: f 128 MET cc_start: 0.6019 (tpp) cc_final: 0.5405 (tpp) REVERT: g 56 PHE cc_start: 0.6927 (m-10) cc_final: 0.6677 (m-10) REVERT: g 71 LYS cc_start: 0.7586 (mttt) cc_final: 0.7200 (mttt) REVERT: g 95 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7879 (tttt) REVERT: m 271 MET cc_start: 0.7933 (tpp) cc_final: 0.7459 (ttp) outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.1571 time to fit residues: 13.3618 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 : 0.491 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 41 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.227931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.182274 restraints weight = 4400.423| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.12 r_work: 0.3897 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4790 Z= 0.102 Angle : 0.501 5.762 6498 Z= 0.258 Chirality : 0.039 0.143 761 Planarity : 0.002 0.026 793 Dihedral : 4.684 55.653 699 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.87 % Allowed : 22.37 % 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: -0.60 (0.36), residues: 571 helix: 2.04 (0.36), residues: 214 sheet: -1.19 (0.50), residues: 109 loop : -2.32 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.007 0.001 PHE m 288 TYR 0.010 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 212) hydrogen bonds : angle 3.32308 ( 597) SS BOND : bond 0.00229 ( 9) SS BOND : angle 0.97592 ( 18) covalent geometry : bond 0.00236 ( 4781) covalent geometry : angle 0.49928 ( 6480) ********************** 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 65 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.495 Fit side-chains REVERT: a 30 LYS cc_start: 0.6754 (ptpt) cc_final: 0.5957 (tptp) REVERT: e 123 MET cc_start: 0.7300 (ptp) cc_final: 0.6836 (ptm) REVERT: f 128 MET cc_start: 0.6099 (tpp) cc_final: 0.5428 (tpp) REVERT: g 56 PHE cc_start: 0.6879 (m-10) cc_final: 0.6641 (m-10) REVERT: g 71 LYS cc_start: 0.7635 (mttt) cc_final: 0.7257 (mttt) REVERT: g 95 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7862 (tttt) REVERT: m 271 MET cc_start: 0.7891 (tpp) cc_final: 0.7491 (ttp) outliers start: 15 outliers final: 14 residues processed: 61 average time/residue: 0.1565 time to fit residues: 12.5518 Evaluate side-chains 62 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.224080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.177868 restraints weight = 4485.557| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.15 r_work: 0.3832 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4790 Z= 0.136 Angle : 0.544 5.711 6498 Z= 0.277 Chirality : 0.041 0.145 761 Planarity : 0.002 0.025 793 Dihedral : 4.923 59.254 699 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.06 % Allowed : 22.18 % 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: -0.75 (0.36), residues: 571 helix: 1.81 (0.36), residues: 214 sheet: -1.18 (0.51), residues: 109 loop : -2.34 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 43 HIS 0.002 0.001 HIS f 61 PHE 0.010 0.001 PHE b 50 TYR 0.015 0.001 TYR n 263 ARG 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 212) hydrogen bonds : angle 3.49104 ( 597) SS BOND : bond 0.00212 ( 9) SS BOND : angle 1.04282 ( 18) covalent geometry : bond 0.00323 ( 4781) covalent geometry : angle 0.54246 ( 6480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.85 seconds wall clock time: 53 minutes 40.22 seconds (3220.22 seconds total)