Starting phenix.real_space_refine on Thu Feb 15 17:36:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/02_2024/6tdw_10469.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/02_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_10469/02_2024/6tdw_10469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/02_2024/6tdw_10469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/02_2024/6tdw_10469.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/02_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.96, 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: 10.76 Conformation dependent library (CDL) restraints added in 1.5 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: 1.02 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: 4.63 Time building geometry restraints manager: 11.08 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: 5182 14.27 - 28.55: 702 28.55 - 42.82: 189 42.82 - 57.10: 72 57.10 - 71.37: 12 Dihedral angle restraints: 6157 sinusoidal: 3416 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 6154 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: 5.400 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: 0.200 Extract box with map and model: 18.970 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.280 Find NCS groups from input model: 0.230 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.360 ------------------------------------------------------------------------------- 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 : 0.970 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: 0.4897 time to fit residues: 113.5790 Evaluate side-chains 94 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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: 0.9980 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 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: 0.7980 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: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6549 Z= 0.218 Angle : 0.615 10.901 8899 Z= 0.308 Chirality : 0.078 1.688 1050 Planarity : 0.005 0.046 1150 Dihedral : 4.594 35.777 887 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.31 % Allowed : 12.35 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 821 helix: 1.15 (0.22), residues: 528 sheet: -3.51 (0.56), residues: 61 loop : -2.72 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 217 HIS 0.003 0.001 HIS A 467 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 : 1.024 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: 0.7889 (m170) cc_final: 0.7624 (m170) REVERT: B 276 ASN cc_start: 0.7536 (t0) cc_final: 0.7099 (t0) REVERT: C 148 LYS cc_start: 0.8565 (tttt) cc_final: 0.8298 (ttpt) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.4646 time to fit residues: 65.8401 Evaluate side-chains 99 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.3518 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= 0.273 Angle : 0.611 10.955 8899 Z= 0.306 Chirality : 0.078 1.710 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.491 40.714 887 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.03 % Allowed : 13.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 821 helix: 1.79 (0.22), residues: 535 sheet: -3.11 (0.61), residues: 57 loop : -2.61 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 217 HIS 0.003 0.001 HIS H 116 PHE 0.020 0.002 PHE B 245 TYR 0.011 0.001 TYR H 25 ARG 0.004 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 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.468 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: A 467 HIS cc_start: 0.8044 (m170) cc_final: 0.7738 (m170) REVERT: B 23 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7854 (tp-100) REVERT: B 276 ASN cc_start: 0.7583 (t0) cc_final: 0.7374 (t0) REVERT: C 112 LYS cc_start: 0.7486 (mttt) cc_final: 0.7125 (ttmt) REVERT: C 148 LYS cc_start: 0.8783 (tttt) cc_final: 0.8516 (ttpt) REVERT: N 102 MET cc_start: 0.6604 (tmm) cc_final: 0.6334 (tmm) outliers start: 14 outliers final: 9 residues processed: 110 average time/residue: 0.4751 time to fit residues: 66.9121 Evaluate side-chains 103 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.3829 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= 0.185 Angle : 0.560 10.977 8899 Z= 0.277 Chirality : 0.077 1.697 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.417 41.410 887 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.74 % Allowed : 13.23 % Favored : 85.03 % 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: 0.83 (0.31), residues: 821 helix: 2.09 (0.22), residues: 535 sheet: -3.05 (0.56), residues: 62 loop : -2.28 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 217 HIS 0.002 0.001 HIS B 335 PHE 0.015 0.001 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.003 0.000 ARG M 233 *********************** 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 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 GLU cc_start: 0.7563 (mp0) cc_final: 0.7004 (mt-10) REVERT: C 112 LYS cc_start: 0.7531 (mttt) cc_final: 0.7135 (ttmt) REVERT: C 148 LYS cc_start: 0.8782 (tttt) cc_final: 0.8566 (ttpt) REVERT: N 102 MET cc_start: 0.6670 (tmm) cc_final: 0.6441 (tmm) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.4813 time to fit residues: 66.3351 Evaluate side-chains 102 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 302 VAL 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 33 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain T residue 52 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6549 Z= 0.245 Angle : 0.590 11.019 8899 Z= 0.295 Chirality : 0.078 1.721 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.437 42.954 887 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.62 % Allowed : 13.81 % Favored : 83.58 % 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: 1.00 (0.31), residues: 821 helix: 2.19 (0.23), residues: 535 sheet: -3.02 (0.54), residues: 62 loop : -2.13 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 217 HIS 0.003 0.001 HIS H 451 PHE 0.020 0.001 PHE B 19 TYR 0.012 0.001 TYR T 51 ARG 0.004 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 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.042 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: 0.8947 (t80) cc_final: 0.8637 (t80) REVERT: B 74 THR cc_start: 0.8264 (p) cc_final: 0.8021 (p) REVERT: B 326 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: C 112 LYS cc_start: 0.7582 (mttt) cc_final: 0.7125 (ttmt) REVERT: C 148 LYS cc_start: 0.8874 (tttt) cc_final: 0.8646 (ttpt) REVERT: N 102 MET cc_start: 0.6853 (tmm) cc_final: 0.6652 (tmm) outliers start: 18 outliers final: 11 residues processed: 114 average time/residue: 0.4423 time to fit residues: 65.4348 Evaluate side-chains 103 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 273 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 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 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: 0.9980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6549 Z= 0.233 Angle : 0.583 11.001 8899 Z= 0.290 Chirality : 0.078 1.712 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.427 46.210 887 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.47 % Allowed : 14.53 % 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: 1.15 (0.31), residues: 821 helix: 2.28 (0.23), residues: 535 sheet: -3.00 (0.52), residues: 62 loop : -1.97 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 48 HIS 0.006 0.001 HIS A 467 PHE 0.017 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.003 0.000 ARG H 317 *********************** 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 118 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.078 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: H 25 TYR cc_start: 0.8972 (t80) cc_final: 0.8630 (t80) REVERT: B 74 THR cc_start: 0.8270 (p) cc_final: 0.8060 (p) REVERT: C 112 LYS cc_start: 0.7606 (mttt) cc_final: 0.7145 (ttmt) REVERT: C 148 LYS cc_start: 0.8904 (tttt) cc_final: 0.8675 (ttpt) outliers start: 17 outliers final: 15 residues processed: 113 average time/residue: 0.4446 time to fit residues: 65.4221 Evaluate side-chains 109 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 273 GLU 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 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 282 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.4878 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= 0.252 Angle : 0.594 11.000 8899 Z= 0.296 Chirality : 0.078 1.720 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.412 49.359 887 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.49 % Allowed : 13.66 % Favored : 82.85 % 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: 1.23 (0.31), residues: 821 helix: 2.31 (0.23), residues: 536 sheet: -2.96 (0.53), residues: 62 loop : -1.88 (0.43), residues: 223 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 245 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG H 317 *********************** 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 126 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.076 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: 0.9008 (t80) cc_final: 0.8663 (t80) REVERT: H 75 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 326 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: C 112 LYS cc_start: 0.7615 (mttt) cc_final: 0.7120 (ttmt) REVERT: C 148 LYS cc_start: 0.8935 (tttt) cc_final: 0.8710 (ttpt) outliers start: 24 outliers final: 21 residues processed: 118 average time/residue: 0.4333 time to fit residues: 66.8011 Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 348 VAL 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 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 B residue 312 ARG 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 Chi-restraints excluded: chain C residue 165 ILE 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: 0.3980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.4966 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= 0.169 Angle : 0.564 11.009 8899 Z= 0.278 Chirality : 0.078 1.708 1050 Planarity : 0.004 0.042 1150 Dihedral : 4.366 50.317 887 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.62 % Allowed : 15.55 % Favored : 81.83 % 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: 1.44 (0.31), residues: 821 helix: 2.45 (0.23), residues: 536 sheet: -2.83 (0.53), residues: 62 loop : -1.76 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 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 116 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.074 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: H 25 TYR cc_start: 0.8990 (t80) cc_final: 0.8650 (t80) REVERT: H 75 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 112 LYS cc_start: 0.7584 (mttt) cc_final: 0.7137 (ttmt) REVERT: C 148 LYS cc_start: 0.8922 (tttt) cc_final: 0.8697 (ttpt) outliers start: 18 outliers final: 16 residues processed: 109 average time/residue: 0.4858 time to fit residues: 69.1529 Evaluate side-chains 111 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 172 MET 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 291 LEU Chi-restraints excluded: chain B residue 312 ARG 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: 0.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 56 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6549 Z= 0.175 Angle : 0.560 10.999 8899 Z= 0.275 Chirality : 0.078 1.710 1050 Planarity : 0.004 0.043 1150 Dihedral : 4.286 50.999 887 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.62 % Allowed : 15.55 % Favored : 81.83 % 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 (0.32), residues: 821 helix: 2.54 (0.23), residues: 537 sheet: -2.62 (0.56), residues: 60 loop : -1.65 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.023 0.001 PHE B 245 TYR 0.013 0.001 TYR T 51 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 118 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.202 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: H 75 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 112 LYS cc_start: 0.7555 (mttt) cc_final: 0.7117 (ttmt) REVERT: C 148 LYS cc_start: 0.8904 (tttt) cc_final: 0.8689 (ttpt) outliers start: 18 outliers final: 16 residues processed: 112 average time/residue: 0.4572 time to fit residues: 66.8104 Evaluate side-chains 110 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain H residue 469 VAL 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 172 MET 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 291 LEU 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: 0.6980 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5204 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= 0.206 Angle : 0.574 10.988 8899 Z= 0.285 Chirality : 0.078 1.711 1050 Planarity : 0.004 0.043 1150 Dihedral : 4.285 51.940 887 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.33 % Allowed : 15.84 % Favored : 81.83 % 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: 1.63 (0.32), residues: 821 helix: 2.53 (0.23), residues: 538 sheet: -2.65 (0.54), residues: 60 loop : -1.58 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.021 0.001 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.001 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 109 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.955 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: H 75 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 112 LYS cc_start: 0.7557 (mttt) cc_final: 0.7123 (ttmt) REVERT: C 148 LYS cc_start: 0.8942 (tttt) cc_final: 0.8712 (ttpt) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.4619 time to fit residues: 61.9164 Evaluate side-chains 107 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 H residue 348 VAL Chi-restraints excluded: chain H residue 469 VAL 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 172 MET 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 291 LEU 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: 0.9980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.137289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117828 restraints weight = 32889.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122889 restraints weight = 15229.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126110 restraints weight = 9041.707| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5333 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= 0.192 Angle : 0.567 11.007 8899 Z= 0.279 Chirality : 0.077 1.705 1050 Planarity : 0.004 0.043 1150 Dihedral : 4.267 53.170 887 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.62 % Allowed : 15.55 % Favored : 81.83 % 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: 1.75 (0.32), residues: 821 helix: 2.60 (0.23), residues: 538 sheet: -2.52 (0.56), residues: 60 loop : -1.50 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.014 0.001 PHE B 245 TYR 0.007 0.001 TYR B 99 ARG 0.001 0.000 ARG H 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.10 seconds wall clock time: 60 minutes 29.49 seconds (3629.49 seconds total)