Starting phenix.real_space_refine on Thu Mar 13 05:43:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_12520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_12520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_12520.map" model { file = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_12520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7npt_12520/03_2025/7npt_12520.cif" } resolution = 3.27 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.75, per 1000 atoms: 0.55 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: 2.18 Conformation dependent library (CDL) restraints added in 728.5 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: 0.71 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: 2.57 Time building geometry restraints manager: 2.58 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: 1.060 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: 0.150 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- 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= 0.468 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 (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: -1.66 (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 TRP 0.028 0.006 TRPD7 102 HIS 0.011 0.004 HISC1 270 PHE 0.018 0.005 PHEC1 132 TYR 0.028 0.007 TYRC1 207 ARG 0.072 0.009 ARGD7 100 *********************** 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 : 0.633 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: 0.7580 (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: 0.4896 time to fit residues: 74.9002 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.124499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108900 restraints weight = 23291.359| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.19 r_work: 0.3517 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3369 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= 0.270 Angle : 0.694 9.014 6007 Z= 0.374 Chirality : 0.045 0.168 675 Planarity : 0.005 0.053 781 Dihedral : 6.603 28.656 594 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 9.05 % Favored : 90.30 % 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: -0.63 (0.35), residues: 542 helix: -0.56 (0.37), residues: 166 sheet: -0.72 (0.52), residues: 99 loop : -0.02 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPC1 131 HIS 0.005 0.001 HISC1 249 PHE 0.011 0.002 PHEC1 243 TYR 0.014 0.001 TYRC1 336 ARG 0.004 0.001 ARGC1 380 *********************** 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 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.656 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: C1 108 MET cc_start: 0.7527 (mmm) cc_final: 0.6876 (mtt) REVERT: C1 185 ASP cc_start: 0.7592 (p0) cc_final: 0.7181 (t0) REVERT: C1 234 MET cc_start: 0.7909 (tpp) cc_final: 0.7036 (tpt) REVERT: D7 26 MET cc_start: 0.7562 (mmm) cc_final: 0.7329 (mmm) REVERT: D7 111 ARG cc_start: 0.4621 (mtt180) cc_final: 0.2926 (ttt180) REVERT: D7 116 ILE cc_start: 0.7825 (pt) cc_final: 0.7609 (pt) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.4289 time to fit residues: 35.2002 Evaluate side-chains 64 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 21 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.121451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105629 restraints weight = 23774.975| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.31 r_work: 0.3469 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.224 Angle : 0.597 8.207 6007 Z= 0.316 Chirality : 0.044 0.150 675 Planarity : 0.005 0.068 781 Dihedral : 5.967 24.886 594 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 8.41 % Favored : 89.66 % 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: -0.09 (0.36), residues: 542 helix: 0.71 (0.41), residues: 155 sheet: -0.68 (0.51), residues: 101 loop : -0.13 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 220 HIS 0.003 0.001 HISC1 133 PHE 0.009 0.001 PHEC1 301 TYR 0.012 0.002 TYRC1 336 ARG 0.005 0.001 ARGC1 291 *********************** 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 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.142 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: 0.7518 (mmm) cc_final: 0.7046 (mtt) REVERT: C1 185 ASP cc_start: 0.7482 (p0) cc_final: 0.6963 (t0) REVERT: C1 234 MET cc_start: 0.7835 (tpp) cc_final: 0.7097 (tpt) REVERT: C1 285 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6908 (ttt) REVERT: D7 26 MET cc_start: 0.7590 (mmm) cc_final: 0.7356 (mmm) REVERT: D7 111 ARG cc_start: 0.4823 (mtt180) cc_final: 0.3184 (ttt180) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.5541 time to fit residues: 44.0108 Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 D8 residue 26 MET Chi-restraints excluded: chain D8 residue 89 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 297 GLN D7 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103651 restraints weight = 23763.477| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.30 r_work: 0.3436 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4416 Z= 0.312 Angle : 0.627 8.087 6007 Z= 0.334 Chirality : 0.045 0.169 675 Planarity : 0.005 0.047 781 Dihedral : 5.985 24.146 594 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.59 % Allowed : 10.34 % Favored : 87.07 % 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: -0.26 (0.35), residues: 542 helix: 0.79 (0.41), residues: 155 sheet: -0.67 (0.53), residues: 93 loop : -0.45 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 220 HIS 0.003 0.001 HISC1 249 PHE 0.011 0.002 PHEC1 301 TYR 0.008 0.001 TYRC1 336 ARG 0.004 0.001 ARGC1 151 *********************** 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 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.127 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: 0.7697 (mmm) cc_final: 0.7031 (mtt) REVERT: C1 185 ASP cc_start: 0.7625 (p0) cc_final: 0.6891 (t0) REVERT: C1 234 MET cc_start: 0.7938 (tpp) cc_final: 0.7268 (tpt) REVERT: C1 403 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D7 111 ARG cc_start: 0.4926 (mtt180) cc_final: 0.3255 (ttt180) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.4912 time to fit residues: 38.3489 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 : 0.727 ------------------------------------------------------------------------------- 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 C1 residue 403 GLU Chi-restraints excluded: chain D7 residue 19 GLN Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 46 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 53 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.121901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106091 restraints weight = 23553.851| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.29 r_work: 0.3476 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4644 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= 0.173 Angle : 0.552 7.497 6007 Z= 0.287 Chirality : 0.043 0.147 675 Planarity : 0.004 0.043 781 Dihedral : 5.556 23.898 594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 11.85 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.36), residues: 542 helix: 1.25 (0.42), residues: 155 sheet: -0.71 (0.51), residues: 101 loop : -0.30 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 270 PHE 0.007 0.001 PHEC1 307 TYR 0.007 0.001 TYRC1 336 ARG 0.003 0.000 ARGC1 310 *********************** 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 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.715 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: 0.7641 (mmm) cc_final: 0.7028 (mtt) REVERT: C1 185 ASP cc_start: 0.7706 (p0) cc_final: 0.6976 (t0) REVERT: C1 234 MET cc_start: 0.7861 (tpp) cc_final: 0.7226 (tpt) REVERT: D7 111 ARG cc_start: 0.4912 (mtt180) cc_final: 0.3209 (ttt180) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.4624 time to fit residues: 33.6472 Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 D8 residue 22 VAL Chi-restraints excluded: chain D8 residue 26 MET 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 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.122078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106312 restraints weight = 23362.830| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.28 r_work: 0.3481 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4416 Z= 0.183 Angle : 0.542 7.047 6007 Z= 0.278 Chirality : 0.043 0.145 675 Planarity : 0.004 0.041 781 Dihedral : 5.295 23.684 594 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 12.50 % 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 (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: 0.32 (0.36), residues: 542 helix: 1.83 (0.43), residues: 149 sheet: -0.76 (0.52), residues: 101 loop : -0.21 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 133 PHE 0.007 0.001 PHEC1 307 TYR 0.006 0.001 TYRC1 336 ARG 0.003 0.000 ARGC1 310 *********************** 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 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7614 (mmm) cc_final: 0.7020 (mtt) REVERT: C1 234 MET cc_start: 0.7841 (tpp) cc_final: 0.7510 (tpt) REVERT: C1 265 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7515 (m) REVERT: D7 111 ARG cc_start: 0.5063 (mtt180) cc_final: 0.3341 (ttt180) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.4516 time to fit residues: 32.1682 Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 175 THR Chi-restraints excluded: chain C1 residue 265 VAL Chi-restraints excluded: chain D8 residue 22 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104728 restraints weight = 23633.346| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.29 r_work: 0.3458 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4416 Z= 0.256 Angle : 0.575 7.414 6007 Z= 0.300 Chirality : 0.044 0.148 675 Planarity : 0.004 0.044 781 Dihedral : 5.443 23.664 594 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.37 % Allowed : 12.28 % 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 (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: 0.19 (0.37), residues: 542 helix: 1.91 (0.43), residues: 143 sheet: -0.89 (0.53), residues: 102 loop : -0.33 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPC1 131 HIS 0.003 0.001 HISC1 133 PHE 0.011 0.001 PHEC1 301 TYR 0.006 0.001 TYRD7 96 ARG 0.003 0.000 ARGC1 151 *********************** 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 64 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7669 (mmm) cc_final: 0.7013 (mtt) REVERT: C1 109 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7525 (tp) REVERT: C1 234 MET cc_start: 0.7873 (tpp) cc_final: 0.7534 (tpt) REVERT: C1 285 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6954 (ttp) REVERT: D7 111 ARG cc_start: 0.5000 (mtt180) cc_final: 0.3299 (ttt180) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.4321 time to fit residues: 30.1905 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 : 0.689 ------------------------------------------------------------------------------- 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 399 VAL Chi-restraints excluded: chain D8 residue 22 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.121428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105568 restraints weight = 23740.293| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.30 r_work: 0.3472 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5073 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= 0.207 Angle : 0.542 7.243 6007 Z= 0.280 Chirality : 0.043 0.147 675 Planarity : 0.004 0.043 781 Dihedral : 5.252 23.528 594 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 (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: 0.27 (0.37), residues: 542 helix: 2.10 (0.43), residues: 143 sheet: -0.93 (0.52), residues: 102 loop : -0.31 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPC1 357 HIS 0.001 0.001 HISC1 249 PHE 0.008 0.001 PHEC1 301 TYR 0.006 0.001 TYRC1 336 ARG 0.003 0.000 ARGC1 310 *********************** 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 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.641 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: 0.7645 (mmm) cc_final: 0.7023 (mtt) REVERT: C1 109 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7474 (tp) REVERT: C1 234 MET cc_start: 0.7828 (tpp) cc_final: 0.7508 (tpt) REVERT: C1 285 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6870 (ttp) REVERT: D7 111 ARG cc_start: 0.4995 (mtt180) cc_final: 0.3213 (ttt180) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.4370 time to fit residues: 29.9816 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 D8 residue 22 VAL 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 42 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.122224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107058 restraints weight = 23806.854| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.44 r_work: 0.3483 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.004 0.078 4416 Z= 0.285 Angle : 0.583 7.550 6007 Z= 0.305 Chirality : 0.044 0.154 675 Planarity : 0.005 0.046 781 Dihedral : 5.494 23.446 594 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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 (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: 0.05 (0.37), residues: 542 helix: 1.86 (0.43), residues: 144 sheet: -1.03 (0.53), residues: 102 loop : -0.45 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPC1 131 HIS 0.003 0.001 HISC1 133 PHE 0.009 0.001 PHEC1 301 TYR 0.006 0.001 TYRD7 96 ARG 0.003 0.000 ARGC1 151 *********************** 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.661 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: 0.7652 (mmm) cc_final: 0.7094 (mtt) REVERT: C1 109 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7643 (tp) REVERT: C1 234 MET cc_start: 0.7782 (tpp) cc_final: 0.7373 (tpt) REVERT: C1 285 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6873 (ttp) REVERT: D7 38 ASP cc_start: 0.6066 (m-30) cc_final: 0.5809 (m-30) REVERT: D7 111 ARG cc_start: 0.5128 (mtt180) cc_final: 0.3354 (ttt180) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.4555 time to fit residues: 29.7576 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 D8 residue 22 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 16 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 44 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: C1 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109455 restraints weight = 23192.435| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.09 r_work: 0.3540 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4416 Z= 0.155 Angle : 0.518 6.820 6007 Z= 0.266 Chirality : 0.043 0.143 675 Planarity : 0.004 0.041 781 Dihedral : 5.044 23.120 594 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 12.72 % 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 (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: 0.43 (0.37), residues: 542 helix: 2.37 (0.43), residues: 144 sheet: -1.13 (0.50), residues: 107 loop : -0.15 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPC1 357 HIS 0.002 0.000 HISC1 270 PHE 0.008 0.001 PHEC1 307 TYR 0.005 0.001 TYRC1 336 ARG 0.003 0.000 ARGC1 310 ********************** 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 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.668 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: 0.7509 (mmm) cc_final: 0.7021 (mtt) REVERT: C1 109 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7536 (tp) REVERT: C1 234 MET cc_start: 0.7693 (tpp) cc_final: 0.7384 (tpt) REVERT: D7 38 ASP cc_start: 0.5852 (m-30) cc_final: 0.5608 (m-30) REVERT: D7 111 ARG cc_start: 0.5015 (mtt180) cc_final: 0.3340 (ttt180) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.4347 time to fit residues: 29.8070 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 289 SER Chi-restraints excluded: chain C1 residue 310 ARG Chi-restraints excluded: chain D8 residue 22 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 37 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.123483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108163 restraints weight = 23673.000| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.46 r_work: 0.3490 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4416 Z= 0.235 Angle : 0.553 6.956 6007 Z= 0.287 Chirality : 0.044 0.150 675 Planarity : 0.004 0.043 781 Dihedral : 5.208 22.935 594 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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 (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: 0.29 (0.37), residues: 542 helix: 2.20 (0.43), residues: 144 sheet: -1.08 (0.52), residues: 97 loop : -0.31 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 357 HIS 0.002 0.001 HISD8 118 PHE 0.008 0.001 PHEC1 307 TYR 0.006 0.001 TYRC1 287 ARG 0.003 0.000 ARGD8 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.26 seconds wall clock time: 87 minutes 29.26 seconds (5249.26 seconds total)