Starting phenix.real_space_refine on Tue Mar 3 20:48:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2026/7npt_12520.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 2737 2.51 5 N 753 2.21 5 O 809 1.98 5 H 4288 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8609 Number of models: 1 Model: "" Number of chains: 3 Chain: "C1" Number of atoms: 5343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5343 Classifications: {'peptide': 339} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 313} Chain breaks: 2 Chain: "D7" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1715 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "D8" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1551 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 1.51, per 1000 atoms: 0.18 Number of scatterers: 8609 At special positions: 0 Unit cell: (92.4, 99, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 809 8.00 N 753 7.00 C 2737 6.00 H 4288 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 133.7 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 5 sheets defined 34.1% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C1' and resid 98 through 133 removed outlier: 4.218A pdb=" N ALAC1 102 " --> pdb=" O PROC1 98 " (cutoff:3.500A) Processing helix chain 'C1' and resid 135 through 139 Processing helix chain 'C1' and resid 189 through 203 Processing helix chain 'C1' and resid 216 through 218 No H-bonds generated for 'chain 'C1' and resid 216 through 218' Processing helix chain 'C1' and resid 226 through 245 Processing helix chain 'C1' and resid 263 through 267 removed outlier: 3.605A pdb=" N TRPC1 267 " --> pdb=" O TRPC1 264 " (cutoff:3.500A) Processing helix chain 'C1' and resid 268 through 272 Processing helix chain 'C1' and resid 289 through 302 removed outlier: 3.554A pdb=" N ALAC1 295 " --> pdb=" O ARGC1 291 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAC1 298 " --> pdb=" O ALAC1 294 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLUC1 299 " --> pdb=" O ALAC1 295 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEUC1 300 " --> pdb=" O GLUC1 296 " (cutoff:3.500A) Processing helix chain 'C1' and resid 313 through 317 removed outlier: 3.662A pdb=" N ALAC1 316 " --> pdb=" O SERC1 313 " (cutoff:3.500A) Processing helix chain 'C1' and resid 331 through 333 No H-bonds generated for 'chain 'C1' and resid 331 through 333' Processing helix chain 'C1' and resid 334 through 340 Processing helix chain 'C1' and resid 360 through 362 No H-bonds generated for 'chain 'C1' and resid 360 through 362' Processing helix chain 'C1' and resid 400 through 413 removed outlier: 3.503A pdb=" N LYSC1 410 " --> pdb=" O GLUC1 406 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLNC1 413 " --> pdb=" O GLNC1 409 " (cutoff:3.500A) Processing helix chain 'D7' and resid 28 through 30 No H-bonds generated for 'chain 'D7' and resid 28 through 30' Processing helix chain 'D7' and resid 42 through 47 removed outlier: 3.747A pdb=" N METD7 46 " --> pdb=" O PROD7 42 " (cutoff:3.500A) Processing helix chain 'D7' and resid 48 through 61 removed outlier: 3.680A pdb=" N LYSD7 52 " --> pdb=" O ASPD7 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALD7 53 " --> pdb=" O PROD7 49 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLUD7 60 " --> pdb=" O SERD7 56 " (cutoff:3.500A) Processing helix chain 'D7' and resid 120 through 128 removed outlier: 3.535A pdb=" N SERD7 125 " --> pdb=" O THRD7 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASPD7 126 " --> pdb=" O ALAD7 122 " (cutoff:3.500A) Processing helix chain 'D8' and resid 42 through 45 Processing helix chain 'D8' and resid 46 through 62 removed outlier: 3.518A pdb=" N GLUD8 60 " --> pdb=" O SERD8 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C1' and resid 3 through 4 removed outlier: 6.137A pdb=" N ARGC1 3 " --> pdb=" O ARGC1 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C1' and resid 19 through 22 removed outlier: 7.120A pdb=" N GLUC1 19 " --> pdb=" O THRC1 175 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLYC1 177 " --> pdb=" O GLUC1 19 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILEC1 21 " --> pdb=" O GLYC1 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C1' and resid 206 through 214 removed outlier: 5.113A pdb=" N GLYC1 168 " --> pdb=" O ASNC1 208 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLYC1 166 " --> pdb=" O PROC1 210 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N METC1 212 " --> pdb=" O ARGC1 164 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARGC1 164 " --> pdb=" O METC1 212 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SERC1 214 " --> pdb=" O VALC1 162 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VALC1 162 " --> pdb=" O SERC1 214 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N METC1 169 " --> pdb=" O PHEC1 393 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHEC1 393 " --> pdb=" O METC1 169 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHEC1 392 " --> pdb=" O ALAC1 375 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALAC1 375 " --> pdb=" O PHEC1 392 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEUC1 365 " --> pdb=" O TRPC1 220 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALAC1 222 " --> pdb=" O LEUC1 365 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHEC1 367 " --> pdb=" O ALAC1 222 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VALC1 224 " --> pdb=" O PHEC1 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASPC1 350 " --> pdb=" O TYRC1 221 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N TYRC1 287 " --> pdb=" O METC1 252 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VALC1 254 " --> pdb=" O TYRC1 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D7' and resid 31 through 38 removed outlier: 4.029A pdb=" N ASPD7 99 " --> pdb=" O VALD7 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILED7 103 " --> pdb=" O METD7 26 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARGD7 73 " --> pdb=" O ILED7 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D7' and resid 116 through 118 removed outlier: 8.270A pdb=" N LEUD8 101 " --> pdb=" O VALD8 22 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLYD8 24 " --> pdb=" O LEUD8 101 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILED8 103 " --> pdb=" O GLYD8 24 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N METD8 26 " --> pdb=" O ILED8 103 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N PHED8 105 " --> pdb=" O METD8 26 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 432 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: 1.53 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4285 1.03 - 1.22: 3 1.22 - 1.42: 1817 1.42 - 1.61: 2558 1.61 - 1.81: 41 Bond restraints: 8704 Sorted by residual: bond pdb=" N METC1 1 " pdb=" H1 METC1 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" CB ARGD8 104 " pdb=" CG ARGD8 104 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" C ASNC1 208 " pdb=" N LEUC1 209 " ideal model delta sigma weight residual 1.340 1.230 0.111 5.87e-02 2.90e+02 3.56e+00 bond pdb=" N PROC1 134 " pdb=" CD PROC1 134 " ideal model delta sigma weight residual 1.473 1.453 0.020 1.40e-02 5.10e+03 2.05e+00 bond pdb=" N PROC1 321 " pdb=" CD PROC1 321 " ideal model delta sigma weight residual 1.473 1.453 0.020 1.40e-02 5.10e+03 2.00e+00 ... (remaining 8699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 15621 3.49 - 6.99: 131 6.99 - 10.48: 5 10.48 - 13.97: 0 13.97 - 17.47: 1 Bond angle restraints: 15758 Sorted by residual: angle pdb=" N GLYD8 30 " pdb=" CA GLYD8 30 " pdb=" C GLYD8 30 " ideal model delta sigma weight residual 113.18 130.65 -17.47 2.37e+00 1.78e-01 5.43e+01 angle pdb=" C ALAC1 412 " pdb=" N GLNC1 413 " pdb=" CA GLNC1 413 " ideal model delta sigma weight residual 120.60 127.83 -7.23 1.60e+00 3.91e-01 2.04e+01 angle pdb=" N ARGD8 104 " pdb=" CA ARGD8 104 " pdb=" C ARGD8 104 " ideal model delta sigma weight residual 108.99 114.94 -5.95 1.57e+00 4.06e-01 1.43e+01 angle pdb=" N ALAD8 107 " pdb=" CA ALAD8 107 " pdb=" C ALAD8 107 " ideal model delta sigma weight residual 110.50 115.69 -5.19 1.41e+00 5.03e-01 1.35e+01 angle pdb=" N SERD7 113 " pdb=" CA SERD7 113 " pdb=" C SERD7 113 " ideal model delta sigma weight residual 111.07 114.94 -3.87 1.07e+00 8.73e-01 1.31e+01 ... (remaining 15753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3659 17.80 - 35.60: 252 35.60 - 53.40: 73 53.40 - 71.19: 89 71.19 - 88.99: 10 Dihedral angle restraints: 4083 sinusoidal: 2251 harmonic: 1832 Sorted by residual: dihedral pdb=" CA GLUD7 92 " pdb=" C GLUD7 92 " pdb=" N GLND7 93 " pdb=" CA GLND7 93 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ARGC1 304 " pdb=" C ARGC1 304 " pdb=" N GLYC1 305 " pdb=" CA GLYC1 305 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PROC1 319 " pdb=" C PROC1 319 " pdb=" N THRC1 320 " pdb=" CA THRC1 320 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 4080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 402 0.043 - 0.086: 195 0.086 - 0.129: 61 0.129 - 0.172: 15 0.172 - 0.215: 2 Chirality restraints: 675 Sorted by residual: chirality pdb=" CA THRC1 320 " pdb=" N THRC1 320 " pdb=" C THRC1 320 " pdb=" CB THRC1 320 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILED8 116 " pdb=" N ILED8 116 " pdb=" C ILED8 116 " pdb=" CB ILED8 116 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ILEC1 16 " pdb=" N ILEC1 16 " pdb=" C ILEC1 16 " pdb=" CB ILEC1 16 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 672 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGD7 71 " -0.132 9.50e-02 1.11e+02 5.50e-02 2.67e+01 pdb=" NE ARGD7 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARGD7 71 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARGD7 71 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARGD7 71 " 0.063 2.00e-02 2.50e+03 pdb="HH11 ARGD7 71 " 0.013 2.00e-02 2.50e+03 pdb="HH12 ARGD7 71 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARGD7 71 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARGD7 71 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGD7 100 " 0.096 9.50e-02 1.11e+02 4.65e-02 2.67e+01 pdb=" NE ARGD7 100 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARGD7 100 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARGD7 100 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARGD7 100 " -0.056 2.00e-02 2.50e+03 pdb="HH11 ARGD7 100 " 0.015 2.00e-02 2.50e+03 pdb="HH12 ARGD7 100 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARGD7 100 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARGD7 100 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC1 3 " 0.150 9.50e-02 1.11e+02 5.94e-02 2.58e+01 pdb=" NE ARGC1 3 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARGC1 3 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARGC1 3 " 0.068 2.00e-02 2.50e+03 pdb=" NH2 ARGC1 3 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARGC1 3 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARGC1 3 " -0.015 2.00e-02 2.50e+03 pdb="HH21 ARGC1 3 " -0.028 2.00e-02 2.50e+03 pdb="HH22 ARGC1 3 " 0.044 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 360 2.17 - 2.78: 16482 2.78 - 3.39: 22740 3.39 - 3.99: 28552 3.99 - 4.60: 44384 Nonbonded interactions: 112518 Sorted by model distance: nonbonded pdb=" O ASND8 40 " pdb=" HG SERD8 89 " model vdw 1.563 2.450 nonbonded pdb=" O ALAD8 39 " pdb=" HG1 THRD8 91 " model vdw 1.599 2.450 nonbonded pdb=" OE1 GLNC1 180 " pdb="HD21 ASNC1 181 " model vdw 1.616 2.450 nonbonded pdb=" OD1 ASPC1 350 " pdb=" HG1 THRC1 352 " model vdw 1.626 2.450 nonbonded pdb=" O VALD8 22 " pdb=" H GLYD8 98 " model vdw 1.666 2.450 ... (remaining 112513 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 'D7' and resid 19 through 118) selection = (chain 'D8' and (resid 19 through 117 or (resid 118 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.007 0.111 4416 Z= 0.336 Angle : 1.190 17.466 6007 Z= 0.708 Chirality : 0.055 0.215 675 Planarity : 0.008 0.083 781 Dihedral : 14.114 88.993 1628 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.33), residues: 542 helix: -2.41 (0.30), residues: 153 sheet: -1.03 (0.47), residues: 100 loop : -0.18 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.009 ARGD7 100 TYR 0.028 0.007 TYRC1 207 PHE 0.018 0.005 PHEC1 132 TRP 0.028 0.006 TRPD7 102 HIS 0.011 0.004 HISC1 270 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 4416) covalent geometry : angle 1.19024 ( 6007) hydrogen bonds : bond 0.26497 ( 153) hydrogen bonds : angle 8.69629 ( 432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7712 (mmm) cc_final: 0.7129 (mtt) REVERT: C1 185 ASP cc_start: 0.7581 (p0) cc_final: 0.7324 (t0) REVERT: C1 234 MET cc_start: 0.7618 (tpp) cc_final: 0.6529 (tpt) REVERT: D7 57 ARG cc_start: 0.7449 (tmt-80) cc_final: 0.6260 (mtt180) REVERT: D7 92 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6823 (mt-10) REVERT: D7 93 GLN cc_start: 0.7419 (tp40) cc_final: 0.6210 (mp10) REVERT: D7 111 ARG cc_start: 0.4753 (mtt180) cc_final: 0.3217 (ttt180) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2117 time to fit residues: 32.2068 Evaluate side-chains 69 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 20 ASN C1 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108411 restraints weight = 22746.071| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.16 r_work: 0.3521 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4416 Z= 0.173 Angle : 0.673 8.407 6007 Z= 0.359 Chirality : 0.045 0.167 675 Planarity : 0.005 0.049 781 Dihedral : 6.462 28.806 594 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 8.84 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.35), residues: 542 helix: -0.32 (0.38), residues: 166 sheet: -0.68 (0.51), residues: 99 loop : 0.08 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGC1 151 TYR 0.014 0.002 TYRC1 336 PHE 0.011 0.001 PHEC1 243 TRP 0.015 0.002 TRPC1 131 HIS 0.003 0.001 HISC1 249 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4416) covalent geometry : angle 0.67250 ( 6007) hydrogen bonds : bond 0.06435 ( 153) hydrogen bonds : angle 5.62333 ( 432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7420 (mmm) cc_final: 0.6774 (mtt) REVERT: C1 185 ASP cc_start: 0.7569 (p0) cc_final: 0.7192 (t0) REVERT: C1 234 MET cc_start: 0.7894 (tpp) cc_final: 0.7074 (tpt) REVERT: D7 26 MET cc_start: 0.7452 (mmm) cc_final: 0.7246 (mmm) REVERT: D7 111 ARG cc_start: 0.4519 (mtt180) cc_final: 0.2857 (ttt180) REVERT: D7 116 ILE cc_start: 0.7825 (pt) cc_final: 0.7608 (pt) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.2251 time to fit residues: 18.4814 Evaluate side-chains 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 300 LEU Chi-restraints excluded: chain D8 residue 80 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104890 restraints weight = 23607.254| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.30 r_work: 0.3457 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4416 Z= 0.171 Angle : 0.616 8.304 6007 Z= 0.329 Chirality : 0.044 0.152 675 Planarity : 0.005 0.068 781 Dihedral : 6.038 24.727 594 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 8.84 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.36), residues: 542 helix: 0.67 (0.41), residues: 154 sheet: -0.59 (0.50), residues: 103 loop : -0.15 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGC1 291 TYR 0.012 0.001 TYRC1 336 PHE 0.009 0.001 PHEC1 301 TRP 0.012 0.001 TRPC1 131 HIS 0.004 0.001 HISC1 249 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4416) covalent geometry : angle 0.61601 ( 6007) hydrogen bonds : bond 0.06164 ( 153) hydrogen bonds : angle 5.34841 ( 432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7557 (mmm) cc_final: 0.7070 (mtt) REVERT: C1 185 ASP cc_start: 0.7490 (p0) cc_final: 0.6908 (t0) REVERT: C1 234 MET cc_start: 0.7894 (tpp) cc_final: 0.7173 (tpt) REVERT: D7 26 MET cc_start: 0.7694 (mmm) cc_final: 0.7436 (mmm) REVERT: D7 111 ARG cc_start: 0.4828 (mtt180) cc_final: 0.3186 (ttt180) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1928 time to fit residues: 15.4623 Evaluate side-chains 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 300 LEU Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 80 ASP Chi-restraints excluded: chain D8 residue 89 SER Chi-restraints excluded: chain D8 residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107027 restraints weight = 23509.341| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.09 r_work: 0.3507 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4416 Z= 0.149 Angle : 0.580 7.769 6007 Z= 0.306 Chirality : 0.044 0.152 675 Planarity : 0.005 0.046 781 Dihedral : 5.742 24.342 594 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.80 % Allowed : 9.48 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.36), residues: 542 helix: 1.03 (0.42), residues: 154 sheet: -0.77 (0.50), residues: 103 loop : -0.20 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGC1 310 TYR 0.008 0.001 TYRC1 336 PHE 0.008 0.001 PHEC1 301 TRP 0.009 0.001 TRPC1 131 HIS 0.002 0.001 HISC1 249 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4416) covalent geometry : angle 0.57999 ( 6007) hydrogen bonds : bond 0.05266 ( 153) hydrogen bonds : angle 5.16270 ( 432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7615 (mmm) cc_final: 0.7059 (mtt) REVERT: C1 185 ASP cc_start: 0.7583 (p0) cc_final: 0.6859 (t0) REVERT: C1 234 MET cc_start: 0.7843 (tpp) cc_final: 0.7142 (tpt) REVERT: C1 285 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6934 (ttp) REVERT: C1 403 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: D7 26 MET cc_start: 0.7472 (mmm) cc_final: 0.7216 (mmm) REVERT: D7 111 ARG cc_start: 0.5019 (mtt180) cc_final: 0.3245 (ttt180) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.1957 time to fit residues: 15.0563 Evaluate side-chains 66 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 300 LEU Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain C1 residue 403 GLU Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 80 ASP Chi-restraints excluded: chain D8 residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D7 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.120729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104862 restraints weight = 23680.006| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.29 r_work: 0.3456 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4416 Z= 0.150 Angle : 0.568 7.549 6007 Z= 0.298 Chirality : 0.044 0.149 675 Planarity : 0.005 0.046 781 Dihedral : 5.558 24.175 594 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.80 % Allowed : 12.07 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.36), residues: 542 helix: 1.29 (0.42), residues: 155 sheet: -0.80 (0.51), residues: 102 loop : -0.27 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGC1 310 TYR 0.007 0.001 TYRC1 336 PHE 0.008 0.001 PHEC1 301 TRP 0.008 0.001 TRPC1 131 HIS 0.003 0.001 HISC1 133 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4416) covalent geometry : angle 0.56798 ( 6007) hydrogen bonds : bond 0.05143 ( 153) hydrogen bonds : angle 5.11439 ( 432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7675 (mmm) cc_final: 0.7058 (mtt) REVERT: C1 234 MET cc_start: 0.7884 (tpp) cc_final: 0.7497 (tpt) REVERT: C1 285 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6878 (ttp) REVERT: C1 310 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6575 (mpp-170) REVERT: D7 26 MET cc_start: 0.7604 (mmm) cc_final: 0.7353 (mmm) REVERT: D7 111 ARG cc_start: 0.4909 (mtt180) cc_final: 0.3172 (ttt180) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.2009 time to fit residues: 14.7591 Evaluate side-chains 64 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D7 residue 19 GLN Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 80 ASP Chi-restraints excluded: chain D8 residue 89 SER Chi-restraints excluded: chain D8 residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D7 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104783 restraints weight = 23728.185| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.17 r_work: 0.3463 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4416 Z= 0.181 Angle : 0.589 7.724 6007 Z= 0.309 Chirality : 0.044 0.149 675 Planarity : 0.005 0.048 781 Dihedral : 5.621 24.319 594 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.80 % Allowed : 12.07 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.36), residues: 542 helix: 1.23 (0.42), residues: 155 sheet: -0.89 (0.54), residues: 94 loop : -0.45 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGC1 164 TYR 0.006 0.001 TYRC1 336 PHE 0.008 0.001 PHEC1 301 TRP 0.008 0.001 TRPC1 220 HIS 0.003 0.001 HISC1 133 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4416) covalent geometry : angle 0.58887 ( 6007) hydrogen bonds : bond 0.05358 ( 153) hydrogen bonds : angle 5.20424 ( 432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7677 (mmm) cc_final: 0.7079 (mtt) REVERT: C1 234 MET cc_start: 0.7858 (tpp) cc_final: 0.7207 (tpt) REVERT: C1 285 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7025 (ttp) REVERT: C1 310 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6497 (mpp-170) REVERT: D7 26 MET cc_start: 0.7557 (mmm) cc_final: 0.7313 (mmm) REVERT: D7 111 ARG cc_start: 0.5161 (mtt180) cc_final: 0.3416 (ttt180) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.2034 time to fit residues: 14.6870 Evaluate side-chains 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 80 ASP Chi-restraints excluded: chain D8 residue 89 SER Chi-restraints excluded: chain D8 residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106502 restraints weight = 23663.077| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.29 r_work: 0.3485 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4416 Z= 0.108 Angle : 0.522 7.119 6007 Z= 0.270 Chirality : 0.043 0.144 675 Planarity : 0.004 0.044 781 Dihedral : 5.196 23.643 594 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.37 % Allowed : 12.50 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.37), residues: 542 helix: 1.85 (0.43), residues: 149 sheet: -0.99 (0.49), residues: 111 loop : -0.17 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGC1 164 TYR 0.006 0.001 TYRC1 336 PHE 0.008 0.001 PHEC1 307 TRP 0.010 0.001 TRPC1 357 HIS 0.001 0.001 HISC1 270 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4416) covalent geometry : angle 0.52198 ( 6007) hydrogen bonds : bond 0.04381 ( 153) hydrogen bonds : angle 4.81845 ( 432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7597 (mmm) cc_final: 0.7008 (mtt) REVERT: C1 109 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7470 (tp) REVERT: C1 234 MET cc_start: 0.7807 (tpp) cc_final: 0.7481 (tpt) REVERT: C1 265 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7484 (m) REVERT: C1 285 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6763 (ttp) REVERT: D7 26 MET cc_start: 0.7514 (mmm) cc_final: 0.7308 (mmm) REVERT: D7 111 ARG cc_start: 0.5019 (mtt180) cc_final: 0.3292 (ttt180) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.2037 time to fit residues: 14.2788 Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 109 LEU Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 89 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106831 restraints weight = 23504.761| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.18 r_work: 0.3491 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4416 Z= 0.122 Angle : 0.530 6.957 6007 Z= 0.274 Chirality : 0.043 0.146 675 Planarity : 0.004 0.042 781 Dihedral : 5.136 23.249 594 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 12.50 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.37), residues: 542 helix: 2.18 (0.43), residues: 143 sheet: -1.00 (0.50), residues: 106 loop : -0.14 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGD8 85 TYR 0.005 0.001 TYRC1 336 PHE 0.008 0.001 PHEC1 307 TRP 0.007 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 133 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4416) covalent geometry : angle 0.52982 ( 6007) hydrogen bonds : bond 0.04486 ( 153) hydrogen bonds : angle 4.80883 ( 432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7619 (mmm) cc_final: 0.7049 (mtt) REVERT: C1 109 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7507 (tp) REVERT: C1 234 MET cc_start: 0.7819 (tpp) cc_final: 0.7521 (tpt) REVERT: C1 285 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6778 (ttp) REVERT: D7 26 MET cc_start: 0.7531 (mmm) cc_final: 0.7264 (mmm) REVERT: D7 38 ASP cc_start: 0.5897 (m-30) cc_final: 0.5636 (m-30) REVERT: D7 111 ARG cc_start: 0.4945 (mtt180) cc_final: 0.3198 (ttt180) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1916 time to fit residues: 12.4116 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 109 LEU Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 89 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106391 restraints weight = 23752.641| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.21 r_work: 0.3482 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4416 Z= 0.137 Angle : 0.539 7.048 6007 Z= 0.279 Chirality : 0.043 0.147 675 Planarity : 0.004 0.043 781 Dihedral : 5.179 23.406 594 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.72 % Allowed : 12.72 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.37), residues: 542 helix: 2.20 (0.43), residues: 144 sheet: -0.95 (0.53), residues: 97 loop : -0.23 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGC1 151 TYR 0.004 0.001 TYRC1 336 PHE 0.009 0.001 PHEC1 301 TRP 0.009 0.001 TRPC1 357 HIS 0.001 0.001 HISC1 133 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4416) covalent geometry : angle 0.53872 ( 6007) hydrogen bonds : bond 0.04663 ( 153) hydrogen bonds : angle 4.86135 ( 432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7627 (mmm) cc_final: 0.7067 (mtt) REVERT: C1 109 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7558 (tp) REVERT: C1 234 MET cc_start: 0.7799 (tpp) cc_final: 0.7487 (tpt) REVERT: C1 285 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6570 (ttp) REVERT: D7 26 MET cc_start: 0.7500 (mmm) cc_final: 0.7284 (mmm) REVERT: D7 38 ASP cc_start: 0.5837 (m-30) cc_final: 0.5623 (m-30) REVERT: D7 111 ARG cc_start: 0.4906 (mtt180) cc_final: 0.3177 (ttt180) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.2063 time to fit residues: 13.8348 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 109 LEU Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.109412 restraints weight = 23536.567| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.46 r_work: 0.3508 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4416 Z= 0.118 Angle : 0.524 6.885 6007 Z= 0.270 Chirality : 0.043 0.145 675 Planarity : 0.004 0.042 781 Dihedral : 5.038 23.134 594 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.37), residues: 542 helix: 2.31 (0.43), residues: 144 sheet: -1.02 (0.52), residues: 97 loop : -0.16 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGD8 85 TYR 0.004 0.001 TYRD7 96 PHE 0.008 0.001 PHEC1 307 TRP 0.010 0.001 TRPC1 357 HIS 0.001 0.001 HISC1 270 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4416) covalent geometry : angle 0.52405 ( 6007) hydrogen bonds : bond 0.04361 ( 153) hydrogen bonds : angle 4.71470 ( 432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7561 (mmm) cc_final: 0.7090 (mtt) REVERT: C1 109 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7586 (tp) REVERT: C1 234 MET cc_start: 0.7711 (tpp) cc_final: 0.7426 (tpt) REVERT: C1 285 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6577 (ttp) REVERT: D7 38 ASP cc_start: 0.5934 (m-30) cc_final: 0.5712 (m-30) REVERT: D7 111 ARG cc_start: 0.5013 (mtt180) cc_final: 0.3270 (ttt180) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.2097 time to fit residues: 13.1691 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 109 LEU Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 285 MET Chi-restraints excluded: chain C1 residue 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain C1 residue 399 VAL Chi-restraints excluded: chain D8 residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.124216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109140 restraints weight = 23499.930| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.45 r_work: 0.3507 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4416 Z= 0.126 Angle : 0.528 6.825 6007 Z= 0.273 Chirality : 0.043 0.148 675 Planarity : 0.004 0.042 781 Dihedral : 5.034 22.937 594 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.51 % Allowed : 13.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.37), residues: 542 helix: 2.28 (0.43), residues: 144 sheet: -0.99 (0.52), residues: 97 loop : -0.19 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGD8 112 TYR 0.005 0.001 TYRC1 287 PHE 0.008 0.001 PHEC1 307 TRP 0.009 0.001 TRPC1 357 HIS 0.001 0.001 HISC1 133 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4416) covalent geometry : angle 0.52756 ( 6007) hydrogen bonds : bond 0.04473 ( 153) hydrogen bonds : angle 4.73175 ( 432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.23 seconds wall clock time: 40 minutes 48.72 seconds (2448.72 seconds total)