Starting phenix.real_space_refine on Sun Apr 27 05:30:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc0_36149/04_2025/8jc0_36149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc0_36149/04_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_36149/04_2025/8jc0_36149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc0_36149/04_2025/8jc0_36149.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc0_36149/04_2025/8jc0_36149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc0_36149/04_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-5669/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: 3.45, 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: 1.20 Conformation dependent library (CDL) restraints added in 522.0 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: 0.46 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: 1.05 Time building geometry restraints manager: 1.42 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: 0.340 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.350 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- 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 : 0.475 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1619 time to fit residues: 12.4246 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 : 0.477 ------------------------------------------------------------------------------- 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 = 0.229251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183697 restraints weight = 4387.824| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.27 r_work: 0.3949 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1001 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 9.195 6498 Z= 0.290 Chirality : 0.040 0.144 761 Planarity : 0.003 0.032 793 Dihedral : 4.648 36.963 699 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 0.04154 ( 212) hydrogen bonds : angle 4.32875 ( 597) SS BOND : bond 0.00251 ( 9) SS BOND : angle 1.03877 ( 18) covalent geometry : bond 0.00288 ( 4781) covalent geometry : angle 0.56196 ( 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 : 0.664 Fit side-chains REVERT: a 30 LYS cc_start: 0.7241 (ptpt) cc_final: 0.6064 (tptp) REVERT: d 58 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6449 (tt) REVERT: f 128 MET cc_start: 0.5465 (tpp) cc_final: 0.5200 (tpp) REVERT: g 56 PHE cc_start: 0.7044 (m-10) cc_final: 0.6798 (m-10) REVERT: g 71 LYS cc_start: 0.7442 (mttt) cc_final: 0.7093 (mttt) REVERT: g 95 LYS cc_start: 0.8239 (ttmt) cc_final: 0.8025 (tttt) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1743 time to fit residues: 14.9780 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: 0.6980 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.227499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185338 restraints weight = 4453.955| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.06 r_work: 0.3912 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4790 Z= 0.119 Angle : 0.535 7.307 6498 Z= 0.275 Chirality : 0.040 0.145 761 Planarity : 0.003 0.029 793 Dihedral : 4.694 41.962 699 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.68 % Allowed : 18.74 % Favored : 78.59 % 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: -1.29 (0.36), residues: 571 helix: 1.54 (0.36), residues: 216 sheet: -2.11 (0.46), residues: 120 loop : -2.52 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 43 HIS 0.003 0.001 HIS f 81 PHE 0.006 0.001 PHE e 87 TYR 0.011 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 212) hydrogen bonds : angle 4.03840 ( 597) SS BOND : bond 0.00232 ( 9) SS BOND : angle 1.00545 ( 18) covalent geometry : bond 0.00277 ( 4781) covalent geometry : angle 0.53262 ( 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 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.475 Fit side-chains REVERT: a 30 LYS cc_start: 0.6960 (ptpt) cc_final: 0.5823 (tptp) REVERT: f 128 MET cc_start: 0.5694 (tpp) cc_final: 0.5260 (tpp) REVERT: g 71 LYS cc_start: 0.7480 (mttt) cc_final: 0.7089 (mttt) REVERT: g 95 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7992 (tttt) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1619 time to fit residues: 13.7099 Evaluate side-chains 65 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 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 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: 0.0970 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.227514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183136 restraints weight = 4494.727| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.15 r_work: 0.3892 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4790 Z= 0.115 Angle : 0.527 8.750 6498 Z= 0.269 Chirality : 0.040 0.147 761 Planarity : 0.003 0.026 793 Dihedral : 4.706 44.863 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.82 % Allowed : 18.16 % 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: -1.16 (0.36), residues: 571 helix: 1.64 (0.37), residues: 216 sheet: -1.94 (0.47), residues: 120 loop : -2.49 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 43 HIS 0.002 0.001 HIS f 81 PHE 0.006 0.001 PHE m 288 TYR 0.011 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 212) hydrogen bonds : angle 3.83411 ( 597) SS BOND : bond 0.00213 ( 9) SS BOND : angle 0.96264 ( 18) covalent geometry : bond 0.00268 ( 4781) covalent geometry : angle 0.52518 ( 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: 20 poor density : 55 time to evaluate : 0.516 Fit side-chains REVERT: a 30 LYS cc_start: 0.6998 (ptpt) cc_final: 0.5908 (tptp) REVERT: f 128 MET cc_start: 0.5944 (tpp) cc_final: 0.5387 (tpp) REVERT: g 56 PHE cc_start: 0.6975 (m-10) cc_final: 0.6661 (m-10) REVERT: g 71 LYS cc_start: 0.7444 (mttt) cc_final: 0.7068 (mttt) REVERT: g 95 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7962 (ttmt) outliers start: 20 outliers final: 14 residues processed: 70 average time/residue: 0.1552 time to fit residues: 14.2501 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 : 0.483 ------------------------------------------------------------------------------- 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 71 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 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 = 0.4457 r_free = 0.4457 target = 0.225411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179511 restraints weight = 4534.598| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.23 r_work: 0.3886 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4790 Z= 0.128 Angle : 0.546 7.858 6498 Z= 0.277 Chirality : 0.041 0.150 761 Planarity : 0.003 0.024 793 Dihedral : 4.856 49.577 699 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.63 % Allowed : 19.31 % Favored : 77.06 % 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: -1.14 (0.36), residues: 571 helix: 1.59 (0.36), residues: 216 sheet: -1.73 (0.48), residues: 115 loop : -2.53 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.001 0.001 HIS d 89 PHE 0.008 0.001 PHE b 50 TYR 0.014 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 212) hydrogen bonds : angle 3.77083 ( 597) SS BOND : bond 0.00363 ( 9) SS BOND : angle 1.19114 ( 18) covalent geometry : bond 0.00304 ( 4781) covalent geometry : angle 0.54279 ( 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 74 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.532 Fit side-chains REVERT: a 30 LYS cc_start: 0.6984 (ptpt) cc_final: 0.5888 (tptp) REVERT: a 45 ILE cc_start: 0.8279 (mt) cc_final: 0.8066 (mp) REVERT: f 128 MET cc_start: 0.6093 (tpp) cc_final: 0.5446 (tpp) REVERT: g 71 LYS cc_start: 0.7492 (mttt) cc_final: 0.7102 (mttt) REVERT: g 95 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7939 (ttmt) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.1526 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: 15 poor density : 54 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 n residue 257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 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 = 0.4467 r_free = 0.4467 target = 0.226684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183626 restraints weight = 4497.114| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.12 r_work: 0.3904 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4790 Z= 0.111 Angle : 0.519 6.693 6498 Z= 0.264 Chirality : 0.040 0.146 761 Planarity : 0.002 0.024 793 Dihedral : 4.791 50.824 699 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.63 % Allowed : 20.08 % Favored : 76.29 % 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: -0.88 (0.36), residues: 571 helix: 1.79 (0.36), residues: 214 sheet: -1.57 (0.48), residues: 115 loop : -2.36 (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 0.008 0.001 PHE g 56 TYR 0.011 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 212) hydrogen bonds : angle 3.60368 ( 597) SS BOND : bond 0.00204 ( 9) SS BOND : angle 1.05468 ( 18) covalent geometry : bond 0.00259 ( 4781) covalent geometry : angle 0.51692 ( 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 : 0.475 Fit side-chains REVERT: a 30 LYS cc_start: 0.7087 (ptpt) cc_final: 0.6029 (tptp) REVERT: f 128 MET cc_start: 0.6078 (tpp) cc_final: 0.5455 (tpp) REVERT: g 56 PHE cc_start: 0.7026 (m-10) cc_final: 0.6748 (m-10) REVERT: g 71 LYS cc_start: 0.7629 (mttt) cc_final: 0.7248 (mttt) REVERT: g 95 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7932 (ttmt) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1485 time to fit residues: 13.0257 Evaluate side-chains 67 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 n residue 257 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: 0.2980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 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 = 0.4448 r_free = 0.4448 target = 0.222370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176976 restraints weight = 4486.148| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.10 r_work: 0.3827 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4790 Z= 0.148 Angle : 0.570 6.028 6498 Z= 0.288 Chirality : 0.041 0.152 761 Planarity : 0.003 0.021 793 Dihedral : 5.052 55.391 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.63 % Allowed : 20.65 % 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: -1.04 (0.36), residues: 571 helix: 1.55 (0.36), residues: 214 sheet: -1.55 (0.49), residues: 115 loop : -2.39 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 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 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 212) hydrogen bonds : angle 3.74726 ( 597) SS BOND : bond 0.00213 ( 9) SS BOND : angle 1.12719 ( 18) covalent geometry : bond 0.00352 ( 4781) covalent geometry : angle 0.56766 ( 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 71 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.539 Fit side-chains REVERT: a 30 LYS cc_start: 0.7042 (ptpt) cc_final: 0.6040 (tptp) REVERT: e 123 MET cc_start: 0.7370 (ptp) cc_final: 0.6925 (ptm) REVERT: f 128 MET cc_start: 0.6375 (tpp) cc_final: 0.5551 (tpp) REVERT: g 56 PHE cc_start: 0.7047 (m-10) cc_final: 0.6764 (m-10) REVERT: g 71 LYS cc_start: 0.7632 (mttt) cc_final: 0.7267 (mttt) REVERT: g 95 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7971 (ttmt) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.1528 time to fit residues: 13.5134 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 : 0.552 ------------------------------------------------------------------------------- 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 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: 0.0020 chunk 5 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.227574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184506 restraints weight = 4415.611| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.02 r_work: 0.3923 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2017 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= 0.099 Angle : 0.507 5.688 6498 Z= 0.265 Chirality : 0.039 0.142 761 Planarity : 0.002 0.025 793 Dihedral : 4.817 54.835 699 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.44 % Allowed : 21.22 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.36), residues: 571 helix: 1.83 (0.36), residues: 214 sheet: -1.44 (0.49), residues: 115 loop : -2.31 (0.36), 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 f 87 TYR 0.008 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 212) hydrogen bonds : angle 3.58279 ( 597) SS BOND : bond 0.00224 ( 9) SS BOND : angle 1.01953 ( 18) covalent geometry : bond 0.00226 ( 4781) covalent geometry : angle 0.50491 ( 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 70 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.505 Fit side-chains REVERT: a 30 LYS cc_start: 0.6967 (ptpt) cc_final: 0.5988 (tptp) REVERT: f 128 MET cc_start: 0.6106 (tpp) cc_final: 0.5410 (tpp) REVERT: g 56 PHE cc_start: 0.6908 (m-10) cc_final: 0.6661 (m-10) REVERT: g 71 LYS cc_start: 0.7599 (mttt) cc_final: 0.7219 (mttt) REVERT: g 95 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7900 (ttmt) outliers start: 18 outliers final: 15 residues processed: 65 average time/residue: 0.1577 time to fit residues: 13.6692 Evaluate side-chains 66 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.225033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179585 restraints weight = 4466.809| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.10 r_work: 0.3854 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2103 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= 0.127 Angle : 0.531 5.649 6498 Z= 0.272 Chirality : 0.040 0.145 761 Planarity : 0.002 0.024 793 Dihedral : 4.894 56.676 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.06 % Allowed : 21.80 % Favored : 75.14 % 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: 1.76 (0.36), residues: 214 sheet: -1.38 (0.50), residues: 109 loop : -2.36 (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 b 50 TYR 0.014 0.001 TYR n 263 ARG 0.001 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 212) hydrogen bonds : angle 3.56475 ( 597) SS BOND : bond 0.00214 ( 9) SS BOND : angle 1.01638 ( 18) covalent geometry : bond 0.00301 ( 4781) covalent geometry : angle 0.52871 ( 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 68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.548 Fit side-chains REVERT: a 30 LYS cc_start: 0.6854 (ptpt) cc_final: 0.6018 (tptp) REVERT: e 123 MET cc_start: 0.7176 (ptp) cc_final: 0.6722 (ptm) REVERT: f 128 MET cc_start: 0.6308 (tpp) cc_final: 0.5466 (tpp) REVERT: g 56 PHE cc_start: 0.6995 (m-10) cc_final: 0.6745 (m-10) REVERT: g 71 LYS cc_start: 0.7592 (mttt) cc_final: 0.7200 (mttt) REVERT: g 95 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7904 (ttmt) outliers start: 16 outliers final: 13 residues processed: 65 average time/residue: 0.1594 time to fit residues: 13.7500 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 : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS 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 9 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.0020 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.227189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183306 restraints weight = 4401.085| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.07 r_work: 0.3881 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2149 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= 0.106 Angle : 0.505 5.468 6498 Z= 0.261 Chirality : 0.039 0.142 761 Planarity : 0.002 0.026 793 Dihedral : 4.770 56.306 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.87 % Allowed : 22.75 % 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: -0.70 (0.36), residues: 571 helix: 1.87 (0.37), residues: 214 sheet: -1.20 (0.50), residues: 109 loop : -2.32 (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 0.010 0.001 TYR n 263 ARG 0.001 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 212) hydrogen bonds : angle 3.45431 ( 597) SS BOND : bond 0.00216 ( 9) SS BOND : angle 0.95871 ( 18) covalent geometry : bond 0.00246 ( 4781) covalent geometry : angle 0.50284 ( 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 63 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.534 Fit side-chains REVERT: a 30 LYS cc_start: 0.6799 (ptpt) cc_final: 0.6006 (tptp) REVERT: e 123 MET cc_start: 0.7199 (ptp) cc_final: 0.6719 (ptm) REVERT: f 128 MET cc_start: 0.6253 (tpp) cc_final: 0.5438 (tpp) REVERT: g 56 PHE cc_start: 0.6954 (m-10) cc_final: 0.6739 (m-10) REVERT: g 71 LYS cc_start: 0.7644 (mttt) cc_final: 0.7265 (mttt) REVERT: g 95 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7907 (tttt) outliers start: 15 outliers final: 14 residues processed: 60 average time/residue: 0.1629 time to fit residues: 12.8966 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 32 CYS 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 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: 0.0670 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.226418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.181654 restraints weight = 4492.598| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.05 r_work: 0.3882 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2225 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= 0.112 Angle : 0.512 5.641 6498 Z= 0.264 Chirality : 0.040 0.145 761 Planarity : 0.002 0.025 793 Dihedral : 4.793 57.594 699 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 22.94 % 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: -0.67 (0.36), residues: 571 helix: 1.89 (0.37), residues: 214 sheet: -1.13 (0.51), residues: 109 loop : -2.32 (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 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 212) hydrogen bonds : angle 3.36801 ( 597) SS BOND : bond 0.00200 ( 9) SS BOND : angle 0.97875 ( 18) covalent geometry : bond 0.00263 ( 4781) covalent geometry : angle 0.51056 ( 6480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.97 seconds wall clock time: 53 minutes 52.73 seconds (3232.73 seconds total)