Starting phenix.real_space_refine on Sun Mar 10 21:21:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/03_2024/7r1d_14239.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3279 2.51 5 N 904 2.21 5 O 981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5183 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1549 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 180} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3206 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 382} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 428 Classifications: {'peptide': 56} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.20, per 1000 atoms: 0.62 Number of scatterers: 5183 At special positions: 0 Unit cell: (68.04, 85.05, 99.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 981 8.00 N 904 7.00 C 3279 6.00 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: 1.97 Conformation dependent library (CDL) restraints added in 954.0 milliseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 21.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 96 through 114 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.608A pdb=" N TRP C 126 " --> pdb=" O CYS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.717A pdb=" N LYS C 165 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 199 Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.548A pdb=" N PHE C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 27 Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.253A pdb=" N LEU A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 31' Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.892A pdb=" N ALA A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.116A pdb=" N ILE B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.856A pdb=" N PHE A 93 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.769A pdb=" N MET C 280 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.958A pdb=" N THR C 251 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 245 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 253 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.982A pdb=" N ILE A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 379 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.660A pdb=" N GLN A 48 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 77 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS A 123 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 119 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER A 83 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE A 117 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 133 removed outlier: 5.561A pdb=" N ILE A 139 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 172 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA9, first strand: chain 'A' and resid 230 through 235 removed outlier: 3.737A pdb=" N ALA A 247 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 281 removed outlier: 3.608A pdb=" N CYS A 278 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 311 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.664A pdb=" N ASP A 346 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 366 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.792A pdb=" N ILE B 97 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 104 " --> pdb=" O ILE B 97 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1664 1.34 - 1.45: 788 1.45 - 1.57: 2838 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5317 Sorted by residual: bond pdb=" CA GLU A 286 " pdb=" C GLU A 286 " ideal model delta sigma weight residual 1.523 1.497 0.027 1.80e-02 3.09e+03 2.20e+00 bond pdb=" CB PRO C 173 " pdb=" CG PRO C 173 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" CD1 TYR A 98 " pdb=" CE1 TYR A 98 " ideal model delta sigma weight residual 1.382 1.342 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CB TYR A 98 " pdb=" CG TYR A 98 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.20e-02 2.07e+03 1.49e+00 bond pdb=" CA ILE A 81 " pdb=" C ILE A 81 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.11e+00 ... (remaining 5312 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 183 106.33 - 113.26: 2889 113.26 - 120.19: 1883 120.19 - 127.12: 2171 127.12 - 134.06: 96 Bond angle restraints: 7222 Sorted by residual: angle pdb=" C HIS A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 111.77 9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C LEU C 198 " pdb=" N GLN C 199 " pdb=" CA GLN C 199 " ideal model delta sigma weight residual 122.56 114.04 8.52 1.72e+00 3.38e-01 2.45e+01 angle pdb=" C GLY A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta sigma weight residual 122.41 131.60 -9.19 2.09e+00 2.29e-01 1.93e+01 angle pdb=" CA PRO C 173 " pdb=" N PRO C 173 " pdb=" CD PRO C 173 " ideal model delta sigma weight residual 112.00 106.57 5.43 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA LEU C 212 " pdb=" CB LEU C 212 " pdb=" CG LEU C 212 " ideal model delta sigma weight residual 116.30 128.32 -12.02 3.50e+00 8.16e-02 1.18e+01 ... (remaining 7217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 2844 16.09 - 32.18: 270 32.18 - 48.26: 50 48.26 - 64.35: 18 64.35 - 80.44: 3 Dihedral angle restraints: 3185 sinusoidal: 1288 harmonic: 1897 Sorted by residual: dihedral pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER A 315 " pdb=" C SER A 315 " pdb=" N HIS A 316 " pdb=" CA HIS A 316 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA HIS A 78 " pdb=" C HIS A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 3182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 449 0.033 - 0.067: 194 0.067 - 0.100: 93 0.100 - 0.133: 44 0.133 - 0.167: 3 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA GLN C 199 " pdb=" N GLN C 199 " pdb=" C GLN C 199 " pdb=" CB GLN C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA THR A 28 " pdb=" N THR A 28 " pdb=" C THR A 28 " pdb=" CB THR A 28 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CG LEU C 212 " pdb=" CB LEU C 212 " pdb=" CD1 LEU C 212 " pdb=" CD2 LEU C 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 780 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 172 " 0.084 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 173 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 107 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLY A 107 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 107 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 24 " -0.017 2.00e-02 2.50e+03 1.31e-02 4.31e+00 pdb=" CG TRP A 24 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 24 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 24 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 24 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 24 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 24 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 24 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 24 " -0.009 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 107 2.66 - 3.22: 5036 3.22 - 3.78: 8356 3.78 - 4.34: 11320 4.34 - 4.90: 18569 Nonbonded interactions: 43388 Sorted by model distance: nonbonded pdb=" OG1 THR C 227 " pdb=" OD1 ASN C 274 " model vdw 2.097 2.440 nonbonded pdb=" NE2 GLN A 76 " pdb=" OD1 ASN A 122 " model vdw 2.157 2.520 nonbonded pdb=" OD1 ASP A 379 " pdb=" N PHE A 380 " model vdw 2.180 2.520 nonbonded pdb=" O GLU A 275 " pdb=" OG SER A 293 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR A 284 " pdb=" O PRO A 327 " model vdw 2.190 2.440 ... (remaining 43383 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: 0.830 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: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.005 0.073 5317 Z= 0.318 Angle : 0.795 12.018 7222 Z= 0.432 Chirality : 0.048 0.167 783 Planarity : 0.006 0.124 940 Dihedral : 13.608 80.437 1951 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.31 (0.32), residues: 645 helix: 0.41 (0.49), residues: 121 sheet: -1.10 (0.34), residues: 193 loop : -1.14 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 24 HIS 0.005 0.001 HIS A 64 PHE 0.010 0.001 PHE A 243 TYR 0.021 0.002 TYR A 409 ARG 0.011 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.584 Fit side-chains REVERT: C 109 LEU cc_start: 0.9293 (tp) cc_final: 0.9038 (tp) REVERT: C 111 ASN cc_start: 0.8693 (m-40) cc_final: 0.8381 (m-40) REVERT: C 183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8353 (tt0) REVERT: C 252 TYR cc_start: 0.8183 (m-80) cc_final: 0.7965 (m-80) REVERT: A 33 ASP cc_start: 0.7141 (m-30) cc_final: 0.6819 (m-30) REVERT: A 40 LEU cc_start: 0.9024 (mt) cc_final: 0.8779 (mt) REVERT: A 72 THR cc_start: 0.8702 (m) cc_final: 0.8492 (m) REVERT: A 79 LEU cc_start: 0.8577 (tp) cc_final: 0.8311 (tp) REVERT: A 102 LYS cc_start: 0.7214 (mttt) cc_final: 0.6846 (mttt) REVERT: A 282 ASN cc_start: 0.8648 (t0) cc_final: 0.7842 (t0) REVERT: A 319 GLU cc_start: 0.7109 (tt0) cc_final: 0.6851 (mt-10) REVERT: A 395 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7381 (mm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1958 time to fit residues: 34.7166 Evaluate side-chains 118 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5317 Z= 0.242 Angle : 0.693 10.118 7222 Z= 0.349 Chirality : 0.048 0.159 783 Planarity : 0.005 0.080 940 Dihedral : 5.647 23.501 695 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.93 % Allowed : 10.72 % Favored : 87.35 % 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: -1.17 (0.32), residues: 645 helix: 0.98 (0.48), residues: 116 sheet: -1.30 (0.36), residues: 184 loop : -1.04 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 121 HIS 0.005 0.001 HIS A 316 PHE 0.016 0.001 PHE C 256 TYR 0.018 0.002 TYR C 124 ARG 0.005 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: C 109 LEU cc_start: 0.9312 (tp) cc_final: 0.9042 (tp) REVERT: C 111 ASN cc_start: 0.8700 (m-40) cc_final: 0.8368 (m-40) REVERT: C 163 TRP cc_start: 0.7844 (m100) cc_final: 0.7414 (m100) REVERT: C 192 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.7893 (mtp85) REVERT: A 33 ASP cc_start: 0.7247 (m-30) cc_final: 0.6836 (m-30) REVERT: A 79 LEU cc_start: 0.8588 (tp) cc_final: 0.8298 (tp) REVERT: A 101 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (pp20) REVERT: A 282 ASN cc_start: 0.8633 (t0) cc_final: 0.7836 (t0) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 0.1582 time to fit residues: 26.6222 Evaluate side-chains 121 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5317 Z= 0.259 Angle : 0.674 9.879 7222 Z= 0.340 Chirality : 0.047 0.153 783 Planarity : 0.005 0.067 940 Dihedral : 5.465 25.328 695 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.64 % Allowed : 13.53 % Favored : 83.83 % 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: -1.06 (0.32), residues: 645 helix: 0.98 (0.48), residues: 122 sheet: -1.17 (0.36), residues: 183 loop : -1.01 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 121 HIS 0.005 0.001 HIS A 316 PHE 0.015 0.001 PHE C 256 TYR 0.015 0.002 TYR A 409 ARG 0.004 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.650 Fit side-chains REVERT: C 109 LEU cc_start: 0.9305 (tp) cc_final: 0.9021 (tp) REVERT: C 111 ASN cc_start: 0.8686 (m-40) cc_final: 0.8370 (m-40) REVERT: C 163 TRP cc_start: 0.7822 (m100) cc_final: 0.7297 (m100) REVERT: C 192 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7893 (ptp-110) REVERT: A 33 ASP cc_start: 0.7273 (m-30) cc_final: 0.6819 (m-30) REVERT: A 79 LEU cc_start: 0.8634 (tp) cc_final: 0.8374 (tp) REVERT: A 102 LYS cc_start: 0.7393 (mttt) cc_final: 0.7115 (mttt) REVERT: A 282 ASN cc_start: 0.8718 (t0) cc_final: 0.7879 (t0) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.1919 time to fit residues: 30.5595 Evaluate side-chains 124 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5317 Z= 0.185 Angle : 0.661 11.361 7222 Z= 0.325 Chirality : 0.046 0.172 783 Planarity : 0.004 0.057 940 Dihedral : 5.189 26.788 695 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.11 % Allowed : 15.47 % Favored : 82.43 % 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 (0.32), residues: 645 helix: 1.18 (0.48), residues: 122 sheet: -0.92 (0.36), residues: 177 loop : -1.01 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 121 HIS 0.003 0.001 HIS A 316 PHE 0.016 0.001 PHE C 256 TYR 0.014 0.002 TYR A 409 ARG 0.006 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.642 Fit side-chains REVERT: C 111 ASN cc_start: 0.8669 (m-40) cc_final: 0.8277 (m-40) REVERT: C 115 LEU cc_start: 0.8918 (mm) cc_final: 0.8641 (mm) REVERT: C 127 PHE cc_start: 0.8383 (t80) cc_final: 0.8165 (t80) REVERT: C 163 TRP cc_start: 0.7820 (m100) cc_final: 0.7287 (m100) REVERT: A 33 ASP cc_start: 0.7325 (m-30) cc_final: 0.6855 (m-30) REVERT: A 79 LEU cc_start: 0.8632 (tp) cc_final: 0.8397 (tp) REVERT: A 282 ASN cc_start: 0.8571 (t0) cc_final: 0.7825 (t0) REVERT: A 311 HIS cc_start: 0.7818 (t70) cc_final: 0.7476 (t-90) outliers start: 12 outliers final: 9 residues processed: 135 average time/residue: 0.1635 time to fit residues: 28.7382 Evaluate side-chains 130 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5317 Z= 0.222 Angle : 0.661 11.636 7222 Z= 0.327 Chirality : 0.047 0.183 783 Planarity : 0.004 0.053 940 Dihedral : 5.135 26.661 695 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.64 % Allowed : 16.70 % Favored : 80.67 % 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: -0.82 (0.32), residues: 645 helix: 1.34 (0.48), residues: 122 sheet: -0.80 (0.37), residues: 175 loop : -1.07 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 122 HIS 0.003 0.001 HIS A 64 PHE 0.020 0.001 PHE C 256 TYR 0.013 0.002 TYR A 409 ARG 0.010 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.635 Fit side-chains REVERT: C 111 ASN cc_start: 0.8698 (m-40) cc_final: 0.8403 (m-40) REVERT: C 115 LEU cc_start: 0.8900 (mm) cc_final: 0.8549 (mt) REVERT: C 127 PHE cc_start: 0.8351 (t80) cc_final: 0.8098 (t80) REVERT: C 163 TRP cc_start: 0.7857 (m100) cc_final: 0.7398 (m100) REVERT: C 225 LYS cc_start: 0.7811 (pttm) cc_final: 0.7200 (ptpp) REVERT: A 33 ASP cc_start: 0.7294 (m-30) cc_final: 0.6856 (m-30) REVERT: A 79 LEU cc_start: 0.8653 (tp) cc_final: 0.8452 (tp) REVERT: A 102 LYS cc_start: 0.7202 (mttt) cc_final: 0.7000 (mmtt) REVERT: A 282 ASN cc_start: 0.8642 (t0) cc_final: 0.7887 (t0) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.1728 time to fit residues: 28.9050 Evaluate side-chains 122 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.825 > 50: distance: 55 - 59: 25.990 distance: 59 - 60: 4.223 distance: 60 - 61: 10.457 distance: 60 - 63: 15.385 distance: 61 - 62: 7.955 distance: 61 - 69: 3.823 distance: 66 - 68: 3.333 distance: 67 - 68: 4.039 distance: 69 - 70: 27.159 distance: 70 - 71: 8.068 distance: 70 - 73: 20.444 distance: 71 - 72: 7.694 distance: 71 - 81: 13.454 distance: 73 - 74: 11.594 distance: 74 - 75: 15.860 distance: 75 - 77: 10.935 distance: 76 - 78: 10.677 distance: 77 - 79: 6.146 distance: 78 - 79: 13.267 distance: 79 - 80: 17.965 distance: 81 - 82: 5.403 distance: 82 - 83: 9.844 distance: 82 - 85: 13.019 distance: 83 - 84: 5.794 distance: 83 - 89: 8.154 distance: 85 - 86: 13.785 distance: 86 - 87: 9.087 distance: 86 - 88: 22.206 distance: 89 - 90: 14.110 distance: 90 - 91: 16.469 distance: 90 - 93: 31.811 distance: 91 - 92: 11.691 distance: 91 - 95: 32.170 distance: 93 - 94: 17.866 distance: 95 - 96: 14.709 distance: 96 - 97: 27.051 distance: 96 - 99: 30.428 distance: 97 - 98: 23.212 distance: 97 - 104: 4.678 distance: 99 - 100: 5.495 distance: 100 - 101: 10.781 distance: 101 - 102: 3.994 distance: 101 - 103: 7.596 distance: 104 - 105: 7.239 distance: 105 - 106: 16.013 distance: 105 - 108: 20.238 distance: 106 - 107: 21.159 distance: 106 - 113: 8.172 distance: 109 - 110: 14.454 distance: 110 - 111: 13.957 distance: 111 - 112: 13.552 distance: 113 - 114: 12.448 distance: 114 - 115: 22.706 distance: 115 - 116: 15.298 distance: 115 - 117: 15.840 distance: 117 - 118: 10.090 distance: 118 - 119: 17.399 distance: 118 - 121: 8.777 distance: 119 - 120: 17.465 distance: 119 - 126: 3.295 distance: 121 - 122: 13.661 distance: 122 - 123: 26.802 distance: 123 - 124: 12.736 distance: 123 - 125: 19.352 distance: 126 - 127: 13.052 distance: 127 - 128: 8.388 distance: 127 - 130: 14.092 distance: 128 - 129: 8.526 distance: 128 - 137: 11.247 distance: 130 - 131: 10.439 distance: 131 - 132: 8.721 distance: 131 - 133: 16.236 distance: 132 - 134: 6.995 distance: 134 - 136: 12.194 distance: 135 - 136: 18.985 distance: 137 - 138: 6.895 distance: 138 - 139: 29.122 distance: 139 - 140: 25.369 distance: 139 - 141: 11.502