Starting phenix.real_space_refine on Fri Jan 19 23:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/01_2024/6tdw_10469.pdb" } resolution = 3.8 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= 0.002 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 10 5.16 5 C 4087 2.51 5 N 1105 2.21 5 O 1234 1.98 5 H 6561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12997 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 398 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 3, 'TRANS': 21} Chain: "H" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4014 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 22, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 4830 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2463 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "M" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 639 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 6, 'TRANS': 36} Chain: "N" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 509 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 6.03, per 1000 atoms: 0.46 Number of scatterers: 12997 At special positions: 0 Unit cell: (113.4, 72.45, 107.1, 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 10 16.00 O 1234 8.00 N 1105 7.00 C 4087 6.00 H 6561 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: 11.09 Conformation dependent library (CDL) restraints added in 1.3 seconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 67.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 474 through 487 removed outlier: 5.596A pdb=" N LYS A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 58 removed outlier: 4.020A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 79 Processing helix chain 'H' and resid 81 through 103 Proline residue: H 100 - end of helix Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.378A pdb=" N GLU H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 279 removed outlier: 3.950A pdb=" N MET H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS H 274 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 277 " --> pdb=" O GLU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 removed outlier: 3.782A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 291 " --> pdb=" O PHE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 removed outlier: 3.679A pdb=" N LYS H 296 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 309 through 330 removed outlier: 4.382A pdb=" N VAL H 313 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 358 removed outlier: 3.694A pdb=" N GLU H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP H 355 " --> pdb=" O GLY H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 455 removed outlier: 4.838A pdb=" N GLN H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 453 " --> pdb=" O ALA H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 476 removed outlier: 3.860A pdb=" N SER H 460 " --> pdb=" O PRO H 456 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 464 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 471 " --> pdb=" O THR H 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 472 " --> pdb=" O GLU H 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 56 through 68 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 107 removed outlier: 4.364A pdb=" N SER B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 121 through 164 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 235 through 249 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 65 through 87 Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 131 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'N' and resid 84 through 112 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 9 removed outlier: 5.916A pdb=" N LYS B 4 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 36 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 6 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 38 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 8 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.822A pdb=" N LEU B 50 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER B 268 " --> pdb=" O LEU B 50 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1260 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: 4.47 Time building geometry restraints manager: 11.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6556 1.03 - 1.23: 9 1.23 - 1.42: 2561 1.42 - 1.62: 3969 1.62 - 1.81: 15 Bond restraints: 13110 Sorted by residual: bond pdb=" C LYS C 36 " pdb=" N ASP C 37 " ideal model delta sigma weight residual 1.334 1.175 0.159 1.27e-02 6.20e+03 1.58e+02 bond pdb=" C ASP C 57 " pdb=" N SER C 58 " ideal model delta sigma weight residual 1.333 1.231 0.102 1.26e-02 6.30e+03 6.56e+01 bond pdb=" N VAL H 313 " pdb=" CA VAL H 313 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N VAL H 302 " pdb=" CA VAL H 302 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" N VAL H 312 " pdb=" CA VAL H 312 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.85e+00 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 81.80 - 92.24: 6 92.24 - 102.68: 22 102.68 - 113.12: 16376 113.12 - 123.56: 6439 123.56 - 134.00: 1046 Bond angle restraints: 23889 Sorted by residual: angle pdb=" CG2 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 82.86 25.14 3.00e+00 1.11e-01 7.02e+01 angle pdb=" CD2 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 83.69 24.31 3.00e+00 1.11e-01 6.56e+01 angle pdb=" CD1 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 84.44 23.56 3.00e+00 1.11e-01 6.17e+01 angle pdb=" CA VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 109.00 85.48 23.52 3.00e+00 1.11e-01 6.15e+01 ... (remaining 23884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 5174 14.27 - 28.55: 693 28.55 - 42.82: 174 42.82 - 57.10: 41 57.10 - 71.37: 7 Dihedral angle restraints: 6089 sinusoidal: 3348 harmonic: 2741 Sorted by residual: dihedral pdb=" CA LEU C 29 " pdb=" C LEU C 29 " pdb=" N LYS C 30 " pdb=" CA LYS C 30 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER C 58 " pdb=" C SER C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1048 0.343 - 0.685: 0 0.685 - 1.028: 0 1.028 - 1.370: 0 1.370 - 1.713: 2 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CG LEU M 246 " pdb=" CB LEU M 246 " pdb=" CD1 LEU M 246 " pdb=" CD2 LEU M 246 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CB VAL B 119 " pdb=" CA VAL B 119 " pdb=" CG1 VAL B 119 " pdb=" CG2 VAL B 119 " both_signs ideal model delta sigma weight residual False -2.63 -1.10 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" CA VAL B 73 " pdb=" N VAL B 73 " pdb=" C VAL B 73 " pdb=" CB VAL B 73 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 1047 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 217 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.47e+00 pdb=" N PRO B 218 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 57 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ASP C 57 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP C 57 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 314 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" N ALA H 315 " 0.037 2.00e-02 2.50e+03 pdb=" CA ALA H 315 " -0.010 2.00e-02 2.50e+03 pdb=" H ALA H 315 " -0.016 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1812 2.26 - 2.85: 29645 2.85 - 3.43: 32052 3.43 - 4.02: 41178 4.02 - 4.60: 65451 Nonbonded interactions: 170138 Sorted by model distance: nonbonded pdb=" HG2 GLU H 311 " pdb="HG23 THR C 89 " model vdw 1.678 2.440 nonbonded pdb=" O PRO B 44 " pdb=" HH TYR B 67 " model vdw 1.725 1.850 nonbonded pdb="HH21 ARG H 319 " pdb=" OD1 ASP M 257 " model vdw 1.726 1.850 nonbonded pdb=" O ALA B 305 " pdb=" HG1 THR B 309 " model vdw 1.736 1.850 nonbonded pdb=" OE1 GLN B 240 " pdb="HH11 ARG C 90 " model vdw 1.748 1.850 ... (remaining 170133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.240 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: 0.180 Extract box with map and model: 18.210 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 44.340 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 0.159 6549 Z= 0.497 Angle : 0.839 11.010 8899 Z= 0.465 Chirality : 0.083 1.713 1050 Planarity : 0.005 0.058 1150 Dihedral : 13.713 71.372 2442 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.64 % 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: -1.91 (0.27), residues: 821 helix: -0.17 (0.20), residues: 523 sheet: -3.60 (0.56), residues: 59 loop : -2.97 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 152 HIS 0.006 0.001 HIS A 467 PHE 0.016 0.002 PHE B 223 TYR 0.011 0.002 TYR H 25 ARG 0.006 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ASN cc_start: 0.7669 (t0) cc_final: 0.7302 (t0) REVERT: C 148 LYS cc_start: 0.8632 (tttt) cc_final: 0.8253 (ttpt) REVERT: N 106 LEU cc_start: 0.8104 (mt) cc_final: 0.7819 (mt) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.4797 time to fit residues: 111.7411 Evaluate side-chains 94 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN C 28 HIS C 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6549 Z= 0.216 Angle : 0.616 10.970 8899 Z= 0.308 Chirality : 0.078 1.688 1050 Planarity : 0.005 0.046 1150 Dihedral : 4.602 35.690 887 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.31 % Allowed : 12.50 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.29), residues: 821 helix: 1.13 (0.22), residues: 528 sheet: -3.51 (0.56), residues: 61 loop : -2.74 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 217 HIS 0.004 0.001 HIS H 308 PHE 0.015 0.001 PHE B 19 TYR 0.011 0.001 TYR H 25 ARG 0.003 0.000 ARG H 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 HIS cc_start: 0.7886 (m170) cc_final: 0.7624 (m170) REVERT: B 276 ASN cc_start: 0.7538 (t0) cc_final: 0.7113 (t0) REVERT: C 148 LYS cc_start: 0.8577 (tttt) cc_final: 0.8305 (ttpt) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.5294 time to fit residues: 76.6528 Evaluate side-chains 99 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6549 Z= 0.227 Angle : 0.585 10.962 8899 Z= 0.291 Chirality : 0.078 1.705 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.428 39.447 887 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.03 % Allowed : 13.08 % Favored : 84.88 % 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: 0.45 (0.30), residues: 821 helix: 1.82 (0.22), residues: 535 sheet: -3.07 (0.61), residues: 57 loop : -2.57 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 217 HIS 0.003 0.001 HIS H 116 PHE 0.018 0.001 PHE B 19 TYR 0.009 0.001 TYR H 25 ARG 0.003 0.000 ARG H 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 HIS cc_start: 0.7953 (m170) cc_final: 0.7716 (m170) REVERT: B 23 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7775 (tp-100) REVERT: B 276 ASN cc_start: 0.7518 (t0) cc_final: 0.7265 (t0) REVERT: C 148 LYS cc_start: 0.8738 (tttt) cc_final: 0.8469 (ttpt) REVERT: N 102 MET cc_start: 0.6493 (tmm) cc_final: 0.6211 (tmm) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.4412 time to fit residues: 61.3825 Evaluate side-chains 101 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain T residue 52 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 73 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 64 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: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.209 Angle : 0.567 10.997 8899 Z= 0.282 Chirality : 0.077 1.700 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.410 41.786 887 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.18 % Allowed : 13.37 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 821 helix: 2.14 (0.22), residues: 535 sheet: -3.03 (0.57), residues: 62 loop : -2.28 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.002 0.001 HIS H 116 PHE 0.017 0.001 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.004 0.000 ARG H 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 TYR cc_start: 0.8917 (t80) cc_final: 0.8526 (t80) REVERT: H 318 ASP cc_start: 0.8550 (m-30) cc_final: 0.8315 (m-30) REVERT: C 112 LYS cc_start: 0.7531 (mttt) cc_final: 0.7135 (ttmt) REVERT: C 148 LYS cc_start: 0.8777 (tttt) cc_final: 0.8560 (ttpt) REVERT: N 102 MET cc_start: 0.6697 (tmm) cc_final: 0.6465 (tmm) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.4922 time to fit residues: 69.2182 Evaluate side-chains 101 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.229 Angle : 0.573 10.993 8899 Z= 0.285 Chirality : 0.078 1.716 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.393 44.189 887 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.33 % Allowed : 13.81 % Favored : 83.87 % 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: 1.11 (0.31), residues: 821 helix: 2.28 (0.22), residues: 535 sheet: -2.97 (0.54), residues: 62 loop : -2.10 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.005 0.001 HIS A 467 PHE 0.020 0.001 PHE B 19 TYR 0.011 0.001 TYR T 51 ARG 0.001 0.000 ARG H 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7903 (tp-100) REVERT: B 74 THR cc_start: 0.8223 (p) cc_final: 0.8011 (p) REVERT: B 326 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: C 112 LYS cc_start: 0.7576 (mttt) cc_final: 0.7132 (ttmt) REVERT: C 148 LYS cc_start: 0.8852 (tttt) cc_final: 0.8614 (ttpt) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.4647 time to fit residues: 68.4543 Evaluate side-chains 110 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain T residue 52 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 96 GLN C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6549 Z= 0.293 Angle : 0.617 11.014 8899 Z= 0.310 Chirality : 0.079 1.721 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.470 45.066 887 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.05 % Allowed : 13.95 % Favored : 82.99 % 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: 1.07 (0.31), residues: 821 helix: 2.24 (0.22), residues: 535 sheet: -3.10 (0.52), residues: 62 loop : -2.05 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 217 HIS 0.004 0.001 HIS A 467 PHE 0.019 0.002 PHE B 245 TYR 0.009 0.001 TYR B 99 ARG 0.003 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8011 (tp-100) REVERT: B 326 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: C 112 LYS cc_start: 0.7611 (mttt) cc_final: 0.7150 (ttmt) REVERT: C 148 LYS cc_start: 0.8908 (tttt) cc_final: 0.8681 (ttpt) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.4521 time to fit residues: 65.4182 Evaluate side-chains 106 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.179 Angle : 0.564 11.014 8899 Z= 0.277 Chirality : 0.078 1.709 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.386 46.575 887 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.18 % Allowed : 14.83 % Favored : 82.99 % 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: 1.35 (0.31), residues: 821 helix: 2.42 (0.23), residues: 535 sheet: -2.96 (0.52), residues: 62 loop : -1.84 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.004 0.001 HIS A 475 PHE 0.025 0.001 PHE B 245 TYR 0.010 0.001 TYR T 51 ARG 0.002 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7971 (tp-100) REVERT: C 112 LYS cc_start: 0.7575 (mttt) cc_final: 0.7117 (ttmt) REVERT: C 148 LYS cc_start: 0.8895 (tttt) cc_final: 0.8661 (ttpt) outliers start: 15 outliers final: 14 residues processed: 109 average time/residue: 0.4344 time to fit residues: 61.9909 Evaluate side-chains 105 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.210 Angle : 0.573 10.992 8899 Z= 0.282 Chirality : 0.078 1.715 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.342 48.407 887 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.47 % Allowed : 15.26 % Favored : 82.27 % 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: 1.43 (0.31), residues: 821 helix: 2.46 (0.23), residues: 535 sheet: -2.94 (0.52), residues: 62 loop : -1.75 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 217 HIS 0.003 0.001 HIS A 475 PHE 0.025 0.001 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG N 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 23 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8062 (tp-100) REVERT: C 112 LYS cc_start: 0.7588 (mttt) cc_final: 0.7150 (ttmt) REVERT: C 148 LYS cc_start: 0.8896 (tttt) cc_final: 0.8667 (ttpt) outliers start: 17 outliers final: 17 residues processed: 106 average time/residue: 0.4374 time to fit residues: 60.4345 Evaluate side-chains 109 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.178 Angle : 0.563 11.008 8899 Z= 0.277 Chirality : 0.078 1.711 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.295 49.687 887 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.12 % 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: 1.60 (0.31), residues: 821 helix: 2.58 (0.23), residues: 535 sheet: -2.87 (0.50), residues: 62 loop : -1.65 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 217 HIS 0.003 0.001 HIS A 475 PHE 0.021 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.001 0.000 ARG H 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 TYR cc_start: 0.8997 (t80) cc_final: 0.8697 (t80) REVERT: H 75 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 19 PHE cc_start: 0.8581 (t80) cc_final: 0.8349 (t80) REVERT: C 112 LYS cc_start: 0.7580 (mttt) cc_final: 0.7148 (ttmt) REVERT: C 148 LYS cc_start: 0.8898 (tttt) cc_final: 0.8675 (ttpt) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.4732 time to fit residues: 65.0612 Evaluate side-chains 104 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6549 Z= 0.248 Angle : 0.593 10.979 8899 Z= 0.295 Chirality : 0.078 1.721 1050 Planarity : 0.004 0.041 1150 Dihedral : 4.320 51.356 887 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.18 % Allowed : 15.70 % Favored : 82.12 % 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: 1.51 (0.31), residues: 821 helix: 2.49 (0.23), residues: 536 sheet: -2.94 (0.51), residues: 62 loop : -1.63 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.004 0.001 HIS A 475 PHE 0.021 0.002 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG H 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 TYR cc_start: 0.9031 (t80) cc_final: 0.8647 (t80) REVERT: H 75 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 112 LYS cc_start: 0.7569 (mttt) cc_final: 0.7126 (ttmt) REVERT: C 148 LYS cc_start: 0.8941 (tttt) cc_final: 0.8710 (ttpt) outliers start: 15 outliers final: 13 residues processed: 104 average time/residue: 0.4505 time to fit residues: 61.4346 Evaluate side-chains 103 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.134816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116214 restraints weight = 32509.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121216 restraints weight = 15024.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124319 restraints weight = 8913.553| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.187 Angle : 0.570 11.021 8899 Z= 0.281 Chirality : 0.078 1.706 1050 Planarity : 0.004 0.041 1150 Dihedral : 4.312 52.173 887 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.03 % Allowed : 15.70 % Favored : 82.27 % 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: 1.65 (0.31), residues: 821 helix: 2.59 (0.23), residues: 536 sheet: -2.71 (0.52), residues: 60 loop : -1.60 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.018 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.001 0.000 ARG H 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.70 seconds wall clock time: 60 minutes 45.57 seconds (3645.57 seconds total)