Starting phenix.real_space_refine on Mon Mar 11 15:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_12520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_12520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_12520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_12520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npt_12520/03_2024/7npt_12520.pdb" } 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 Residue "C1 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 19": "OE1" <-> "OE2" Residue "C1 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 150": "OE1" <-> "OE2" Residue "C1 ASP 157": "OD1" <-> "OD2" Residue "C1 PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 173": "OE1" <-> "OE2" Residue "C1 GLU 187": "OE1" <-> "OE2" Residue "C1 GLU 198": "OE1" <-> "OE2" Residue "C1 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 218": "OE1" <-> "OE2" Residue "C1 ASP 248": "OD1" <-> "OD2" Residue "C1 ASP 258": "OD1" <-> "OD2" Residue "C1 ASP 263": "OD1" <-> "OD2" Residue "C1 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 292": "OE1" <-> "OE2" Residue "C1 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 296": "OE1" <-> "OE2" Residue "C1 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 ASP 330": "OD1" <-> "OD2" Residue "C1 ASP 331": "OD1" <-> "OD2" Residue "C1 GLU 335": "OE1" <-> "OE2" Residue "C1 GLU 341": "OE1" <-> "OE2" Residue "C1 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ASP 350": "OD1" <-> "OD2" Residue "C1 ASP 368": "OD1" <-> "OD2" Residue "C1 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 ASP 388": "OD1" <-> "OD2" Residue "C1 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ASP 397": "OD1" <-> "OD2" Residue "C1 GLU 403": "OE1" <-> "OE2" Residue "C1 GLU 405": "OE1" <-> "OE2" Residue "C1 GLU 406": "OE1" <-> "OE2" Residue "C1 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 ASP 38": "OD1" <-> "OD2" Residue "D7 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 GLU 60": "OE1" <-> "OE2" Residue "D7 ASP 80": "OD1" <-> "OD2" Residue "D7 GLU 92": "OE1" <-> "OE2" Residue "D7 ASP 94": "OD1" <-> "OD2" Residue "D7 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ASP 108": "OD1" <-> "OD2" Residue "D7 GLU 110": "OE1" <-> "OE2" Residue "D7 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 GLU 117": "OE1" <-> "OE2" Residue "D7 ASP 126": "OD1" <-> "OD2" Residue "D8 ASP 38": "OD1" <-> "OD2" Residue "D8 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 80": "OD1" <-> "OD2" Residue "D8 GLU 92": "OE1" <-> "OE2" Residue "D8 ASP 94": "OD1" <-> "OD2" Residue "D8 ASP 97": "OD1" <-> "OD2" Residue "D8 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.20, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 6.71 Conformation dependent library (CDL) restraints added in 924.1 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: 0.73 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: 3.04 Time building geometry restraints manager: 6.92 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: 99.38 - 106.33: 199 106.33 - 113.28: 10229 113.28 - 120.23: 2722 120.23 - 127.18: 2523 127.18 - 134.13: 85 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 1.850 nonbonded pdb=" O ALAD8 39 " pdb=" HG1 THRD8 91 " model vdw 1.599 1.850 nonbonded pdb=" OE1 GLNC1 180 " pdb="HD21 ASNC1 181 " model vdw 1.616 1.850 nonbonded pdb=" OD1 ASPC1 350 " pdb=" HG1 THRC1 352 " model vdw 1.626 1.850 nonbonded pdb=" O VALD8 22 " pdb=" H GLYD8 98 " model vdw 1.666 1.850 ... (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 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: 1.420 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: 0.130 Extract box with map and model: 3.640 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.480 Find NCS groups from input model: 0.230 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.700 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: 0.4928 time to fit residues: 75.2605 Evaluate side-chains 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4416 Z= 0.279 Angle : 0.689 8.869 6007 Z= 0.371 Chirality : 0.045 0.167 675 Planarity : 0.005 0.054 781 Dihedral : 6.592 28.461 594 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.65 % Allowed : 9.27 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.35), residues: 542 helix: -0.43 (0.38), residues: 159 sheet: -0.81 (0.50), residues: 98 loop : -0.20 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPC1 131 HIS 0.004 0.001 HISC1 249 PHE 0.010 0.002 PHEC1 301 TYR 0.014 0.001 TYRC1 336 ARG 0.004 0.000 ARGC1 151 *********************** 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 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.754 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: 0.7366 (mmm) cc_final: 0.6787 (mtt) REVERT: C1 185 ASP cc_start: 0.7510 (p0) cc_final: 0.7081 (t0) REVERT: C1 234 MET cc_start: 0.7676 (tpp) cc_final: 0.6747 (tpt) REVERT: D7 26 MET cc_start: 0.7217 (mmm) cc_final: 0.6970 (mmm) REVERT: D7 111 ARG cc_start: 0.4670 (mtt180) cc_final: 0.3213 (ttt180) REVERT: D7 116 ILE cc_start: 0.7704 (pt) cc_final: 0.7470 (pt) REVERT: D8 85 ARG cc_start: 0.7379 (mtp-110) cc_final: 0.7156 (mtp85) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.4619 time to fit residues: 39.1775 Evaluate side-chains 64 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4416 Z= 0.342 Angle : 0.667 8.633 6007 Z= 0.358 Chirality : 0.046 0.161 675 Planarity : 0.006 0.070 781 Dihedral : 6.348 24.828 594 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 9.48 % Favored : 87.50 % 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: -0.56 (0.35), residues: 542 helix: 0.21 (0.40), residues: 155 sheet: -0.55 (0.55), residues: 89 loop : -0.55 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPC1 131 HIS 0.005 0.001 HISC1 249 PHE 0.013 0.002 PHEC1 301 TYR 0.012 0.001 TYRC1 336 ARG 0.005 0.001 ARGC1 164 *********************** 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 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7421 (mmm) cc_final: 0.6918 (mtt) REVERT: C1 234 MET cc_start: 0.7676 (tpp) cc_final: 0.6817 (tpt) REVERT: C1 285 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6948 (ttt) REVERT: C1 403 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: D7 111 ARG cc_start: 0.5085 (mtt180) cc_final: 0.3629 (ttt180) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.4921 time to fit residues: 38.8365 Evaluate side-chains 65 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 368 ASP 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 46 MET Chi-restraints excluded: chain D8 residue 80 ASP 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 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4416 Z= 0.176 Angle : 0.555 7.632 6007 Z= 0.292 Chirality : 0.043 0.146 675 Planarity : 0.004 0.044 781 Dihedral : 5.744 24.957 594 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.16 % Allowed : 11.21 % Favored : 86.64 % 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: 0.97 (0.41), residues: 154 sheet: -0.45 (0.53), residues: 93 loop : -0.42 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 131 HIS 0.002 0.001 HISC1 133 PHE 0.008 0.001 PHEC1 243 TYR 0.007 0.001 TYRC1 336 ARG 0.002 0.000 ARGC1 291 *********************** 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 64 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.716 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: 0.7446 (mmm) cc_final: 0.7017 (mtt) REVERT: C1 234 MET cc_start: 0.7611 (tpp) cc_final: 0.6844 (tpt) REVERT: D7 111 ARG cc_start: 0.5215 (mtt180) cc_final: 0.3698 (ttt180) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.5207 time to fit residues: 35.4827 Evaluate side-chains 61 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 399 VAL Chi-restraints excluded: chain D8 residue 26 MET Chi-restraints excluded: chain D8 residue 46 MET 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 29 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4416 Z= 0.340 Angle : 0.629 7.651 6007 Z= 0.333 Chirality : 0.045 0.153 675 Planarity : 0.005 0.049 781 Dihedral : 5.995 23.594 594 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.02 % Allowed : 13.15 % Favored : 83.84 % 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: -0.36 (0.36), residues: 542 helix: 0.79 (0.41), residues: 155 sheet: -0.66 (0.54), residues: 94 loop : -0.59 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 220 HIS 0.003 0.001 HISC1 133 PHE 0.012 0.002 PHEC1 301 TYR 0.006 0.001 TYRC1 336 ARG 0.004 0.001 ARGD8 112 *********************** 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 67 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7465 (mmm) cc_final: 0.7050 (mtt) REVERT: C1 234 MET cc_start: 0.7680 (tpp) cc_final: 0.7181 (tpt) REVERT: C1 285 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6991 (ttt) REVERT: C1 310 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5740 (mpp-170) REVERT: C1 403 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D7 111 ARG cc_start: 0.5392 (mtt180) cc_final: 0.3835 (ttt180) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.4866 time to fit residues: 34.8695 Evaluate side-chains 63 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 C1 residue 403 GLU Chi-restraints excluded: chain D7 residue 92 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 5 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4416 Z= 0.154 Angle : 0.527 6.710 6007 Z= 0.273 Chirality : 0.043 0.144 675 Planarity : 0.004 0.044 781 Dihedral : 5.360 23.279 594 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.72 % Allowed : 13.36 % 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 (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 (0.36), residues: 542 helix: 1.74 (0.43), residues: 149 sheet: -0.61 (0.51), residues: 101 loop : -0.28 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 270 PHE 0.008 0.001 PHEC1 243 TYR 0.006 0.001 TYRC1 287 ARG 0.002 0.000 ARGC1 164 *********************** 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 62 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7419 (mmm) cc_final: 0.6997 (mtt) REVERT: C1 109 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7465 (tp) REVERT: C1 234 MET cc_start: 0.7542 (tpp) cc_final: 0.6881 (tpt) REVERT: C1 297 GLN cc_start: 0.6589 (mm110) cc_final: 0.6388 (mm110) REVERT: C1 310 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5944 (mpp-170) REVERT: D7 111 ARG cc_start: 0.5406 (mtt180) cc_final: 0.3854 (ttt180) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.5181 time to fit residues: 36.5180 Evaluate side-chains 58 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4416 Z= 0.202 Angle : 0.538 5.923 6007 Z= 0.280 Chirality : 0.043 0.146 675 Planarity : 0.004 0.043 781 Dihedral : 5.281 21.828 594 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.94 % Allowed : 13.36 % Favored : 84.70 % 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: 0.31 (0.37), residues: 542 helix: 1.87 (0.43), residues: 149 sheet: -0.62 (0.54), residues: 94 loop : -0.32 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 133 PHE 0.008 0.001 PHEC1 301 TYR 0.005 0.001 TYRC1 336 ARG 0.002 0.000 ARGD8 112 *********************** 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 61 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7453 (mmm) cc_final: 0.7000 (mtt) REVERT: C1 234 MET cc_start: 0.7574 (tpp) cc_final: 0.7194 (tpt) REVERT: C1 285 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6516 (ttp) REVERT: C1 310 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6393 (mpp-170) REVERT: D7 71 ARG cc_start: 0.4407 (tpt90) cc_final: 0.4200 (tpt170) REVERT: D7 111 ARG cc_start: 0.5229 (mtt180) cc_final: 0.3643 (ttt180) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.4996 time to fit residues: 33.9020 Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D7 residue 92 GLU 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 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5071 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= 0.282 Angle : 0.574 6.084 6007 Z= 0.302 Chirality : 0.044 0.151 675 Planarity : 0.005 0.046 781 Dihedral : 5.533 21.568 594 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.94 % Allowed : 13.79 % Favored : 84.27 % 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: 0.02 (0.37), residues: 542 helix: 1.59 (0.42), residues: 150 sheet: -0.85 (0.52), residues: 104 loop : -0.43 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 357 HIS 0.004 0.001 HISC1 133 PHE 0.013 0.001 PHEC1 301 TYR 0.006 0.001 TYRD7 96 ARG 0.004 0.000 ARGD8 112 *********************** 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 fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.724 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: 0.7537 (mmm) cc_final: 0.7000 (mtt) REVERT: C1 109 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C1 234 MET cc_start: 0.7603 (tpp) cc_final: 0.7204 (tpt) REVERT: D7 111 ARG cc_start: 0.5143 (mtt180) cc_final: 0.3619 (ttt180) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.4890 time to fit residues: 31.7147 Evaluate side-chains 58 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 35 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4416 Z= 0.147 Angle : 0.509 5.614 6007 Z= 0.263 Chirality : 0.042 0.143 675 Planarity : 0.004 0.042 781 Dihedral : 5.036 21.430 594 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.86 % Allowed : 15.09 % Favored : 84.05 % 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: 0.47 (0.37), residues: 542 helix: 2.09 (0.43), residues: 150 sheet: -0.68 (0.51), residues: 106 loop : -0.19 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 270 PHE 0.007 0.001 PHEC1 307 TYR 0.006 0.001 TYRC1 221 ARG 0.002 0.000 ARGC1 415 *********************** 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 fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7396 (mmm) cc_final: 0.6965 (mtt) REVERT: C1 109 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7447 (tp) REVERT: C1 234 MET cc_start: 0.7471 (tpp) cc_final: 0.7189 (tpt) REVERT: C1 285 MET cc_start: 0.6520 (ttp) cc_final: 0.6270 (ttp) REVERT: C1 310 ARG cc_start: 0.6850 (mpp-170) cc_final: 0.6539 (mpp-170) REVERT: D7 111 ARG cc_start: 0.5190 (mtt180) cc_final: 0.3693 (ttt180) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.4875 time to fit residues: 33.0309 Evaluate side-chains 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 D8 residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4416 Z= 0.220 Angle : 0.535 5.511 6007 Z= 0.279 Chirality : 0.043 0.149 675 Planarity : 0.004 0.044 781 Dihedral : 5.175 20.743 594 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.08 % Allowed : 15.09 % Favored : 83.84 % 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: 0.33 (0.37), residues: 542 helix: 1.97 (0.43), residues: 150 sheet: -0.80 (0.51), residues: 107 loop : -0.26 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC1 357 HIS 0.002 0.001 HISC1 133 PHE 0.010 0.001 PHEC1 301 TYR 0.004 0.001 TYRC1 221 ARG 0.003 0.000 ARGD8 112 ********************** 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 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 108 MET cc_start: 0.7463 (mmm) cc_final: 0.6999 (mtt) REVERT: C1 109 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7492 (tp) REVERT: C1 234 MET cc_start: 0.7598 (tpp) cc_final: 0.7256 (tpt) REVERT: C1 285 MET cc_start: 0.6964 (ttp) cc_final: 0.6697 (ttp) REVERT: D7 111 ARG cc_start: 0.5186 (mtt180) cc_final: 0.3616 (ttt180) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.4988 time to fit residues: 31.2235 Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 D8 residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D7 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.123930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108753 restraints weight = 23438.122| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.43 r_work: 0.3499 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4416 Z= 0.157 Angle : 0.504 5.268 6007 Z= 0.260 Chirality : 0.042 0.144 675 Planarity : 0.004 0.041 781 Dihedral : 4.922 20.724 594 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.08 % Allowed : 15.30 % Favored : 83.62 % 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: 0.55 (0.37), residues: 542 helix: 2.18 (0.43), residues: 150 sheet: -0.71 (0.50), residues: 106 loop : -0.12 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPC1 357 HIS 0.001 0.000 HISC1 270 PHE 0.007 0.001 PHEC1 307 TYR 0.005 0.001 TYRC1 221 ARG 0.002 0.000 ARGC1 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.87 seconds wall clock time: 49 minutes 31.08 seconds (2971.08 seconds total)