Starting phenix.real_space_refine on Tue Mar 11 16:33:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.map" model { file = "/net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wre_37775/03_2025/8wre_37775.cif" } resolution = 2.9 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= 1.000 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 42 5.16 5 C 4081 2.51 5 N 1017 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2948 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.76 Number of scatterers: 6328 At special positions: 0 Unit cell: (76.56, 80.96, 134.64, 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 42 16.00 O 1188 8.00 N 1017 7.00 C 4081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 932.0 milliseconds 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: 1526 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 46.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.543A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 126 through 157 removed outlier: 4.936A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.791A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 Processing helix chain 'A' and resid 182 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.939A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.747A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.859A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.534A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.580A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.746A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.387A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 3.672A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.530A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.024A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.698A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.931A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.597A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.771A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.017A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.692A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.063A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.626A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.033A pdb=" N PHE H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP H 100 " --> pdb=" O MET H 111 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET H 111 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.790A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.790A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.901A pdb=" N ILE H 204 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.92 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: 1947 1.34 - 1.46: 1567 1.46 - 1.58: 2899 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6480 Sorted by residual: bond pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.09e+00 bond pdb=" C3 LDP A 601 " pdb=" O1 LDP A 601 " ideal model delta sigma weight residual 1.353 1.373 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C4 LDP A 601 " pdb=" O2 LDP A 601 " ideal model delta sigma weight residual 1.355 1.373 -0.018 2.00e-02 2.50e+03 7.94e-01 bond pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.72e-01 bond pdb=" CG PRO L 95 " pdb=" CD PRO L 95 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.29e-01 ... (remaining 6475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8587 1.34 - 2.67: 165 2.67 - 4.01: 45 4.01 - 5.34: 18 5.34 - 6.68: 3 Bond angle restraints: 8818 Sorted by residual: angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.18 114.72 -4.54 1.56e+00 4.11e-01 8.47e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.50 -5.69 2.21e+00 2.05e-01 6.63e+00 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 117.04 -4.70 2.04e+00 2.40e-01 5.31e+00 angle pdb=" C ILE H 48 " pdb=" N GLY H 49 " pdb=" CA GLY H 49 " ideal model delta sigma weight residual 121.03 117.57 3.46 1.51e+00 4.39e-01 5.24e+00 angle pdb=" C ALA A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta sigma weight residual 123.17 120.00 3.17 1.49e+00 4.50e-01 4.53e+00 ... (remaining 8813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3516 16.42 - 32.83: 262 32.83 - 49.25: 46 49.25 - 65.67: 9 65.67 - 82.09: 3 Dihedral angle restraints: 3836 sinusoidal: 1450 harmonic: 2386 Sorted by residual: dihedral pdb=" CA GLN L 6 " pdb=" C GLN L 6 " pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 61.41 31.59 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA ASP L 143 " pdb=" CB ASP L 143 " pdb=" CG ASP L 143 " pdb=" OD1 ASP L 143 " ideal model delta sinusoidal sigma weight residual -30.00 -89.27 59.27 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 3833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 601 0.029 - 0.058: 256 0.058 - 0.087: 97 0.087 - 0.116: 51 0.116 - 0.145: 12 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1014 not shown) Planarity restraints: 1102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 161 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 236 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 166 " -0.016 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE A 166 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 166 " -0.010 2.00e-02 2.50e+03 ... (remaining 1099 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1425 2.79 - 3.32: 5770 3.32 - 3.85: 10194 3.85 - 4.37: 11691 4.37 - 4.90: 21692 Nonbonded interactions: 50772 Sorted by model distance: nonbonded pdb=" OE1 GLU A 216 " pdb=" OG1 THR L 31 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP L 151 " pdb=" OG SER L 191 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 342 " pdb=" ND2 ASN A 346 " model vdw 2.369 3.120 nonbonded pdb=" O LEU A 133 " pdb=" OG SER A 137 " model vdw 2.385 3.040 ... (remaining 50767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.370 Find NCS groups from input model: 0.080 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.003 0.034 6480 Z= 0.197 Angle : 0.542 6.680 8818 Z= 0.278 Chirality : 0.042 0.145 1017 Planarity : 0.004 0.043 1102 Dihedral : 12.085 82.085 2298 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.24 (0.30), residues: 821 helix: 1.76 (0.29), residues: 330 sheet: 1.24 (0.35), residues: 219 loop : -0.69 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.002 0.000 HIS H 175 PHE 0.019 0.001 PHE A 166 TYR 0.013 0.001 TYR A 433 ARG 0.002 0.000 ARG A 155 *********************** 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 **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.679 Fit side-chains REVERT: A 324 CYS cc_start: 0.8016 (m) cc_final: 0.7811 (m) REVERT: A 433 TYR cc_start: 0.8474 (m-80) cc_final: 0.8260 (m-80) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 1.2547 time to fit residues: 119.8529 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN L 190 ASN L 210 ASN H 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.083381 restraints weight = 8968.498| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.11 r_work: 0.2829 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6480 Z= 0.278 Angle : 0.592 10.044 8818 Z= 0.303 Chirality : 0.044 0.169 1017 Planarity : 0.005 0.044 1102 Dihedral : 4.569 47.715 887 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 6.13 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.38 (0.30), residues: 821 helix: 1.76 (0.29), residues: 333 sheet: 1.52 (0.35), residues: 213 loop : -0.64 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.018 0.002 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.003 0.000 ARG A 274 *********************** 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 **************************** Evaluate side-chains 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.661 Fit side-chains REVERT: A 433 TYR cc_start: 0.8844 (m-80) cc_final: 0.8578 (m-80) REVERT: L 211 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7797 (ttm170) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 1.4006 time to fit residues: 127.5851 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 157 ASN Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 ASN L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.084123 restraints weight = 9032.027| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.12 r_work: 0.2850 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6480 Z= 0.214 Angle : 0.559 10.216 8818 Z= 0.284 Chirality : 0.042 0.174 1017 Planarity : 0.005 0.045 1102 Dihedral : 4.418 44.818 887 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.71 % Allowed : 9.54 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.45 (0.30), residues: 821 helix: 1.85 (0.30), residues: 335 sheet: 1.44 (0.35), residues: 216 loop : -0.59 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.015 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.009 0.000 ARG A 274 *********************** 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 **************************** Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.767 Fit side-chains REVERT: A 433 TYR cc_start: 0.8821 (m-80) cc_final: 0.8558 (m-80) REVERT: L 156 GLN cc_start: 0.8033 (mp10) cc_final: 0.7827 (mp10) REVERT: H 89 ASP cc_start: 0.8884 (t70) cc_final: 0.8648 (t0) outliers start: 12 outliers final: 3 residues processed: 81 average time/residue: 1.5985 time to fit residues: 135.1081 Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3274 > 50: distance: 3 - 90: 16.223 distance: 14 - 93: 26.033 distance: 44 - 53: 3.203 distance: 64 - 86: 28.274 distance: 67 - 83: 28.983 distance: 79 - 83: 29.057 distance: 83 - 84: 7.630 distance: 84 - 85: 10.543 distance: 84 - 87: 16.567 distance: 85 - 86: 27.193 distance: 85 - 90: 21.423 distance: 87 - 88: 30.795 distance: 87 - 89: 30.856 distance: 90 - 91: 23.432 distance: 91 - 92: 18.814 distance: 91 - 94: 33.202 distance: 92 - 93: 24.596 distance: 92 - 97: 10.499 distance: 94 - 95: 24.359 distance: 94 - 96: 43.342 distance: 97 - 98: 16.100 distance: 98 - 99: 20.857 distance: 98 - 101: 25.912 distance: 99 - 100: 8.743 distance: 99 - 104: 16.071 distance: 101 - 102: 25.630 distance: 101 - 103: 23.064 distance: 104 - 105: 31.578 distance: 105 - 106: 19.568 distance: 105 - 108: 35.619 distance: 106 - 110: 8.502 distance: 108 - 109: 38.346 distance: 110 - 111: 6.512 distance: 111 - 112: 28.476 distance: 111 - 114: 23.290 distance: 112 - 113: 21.909 distance: 112 - 116: 23.407 distance: 114 - 115: 38.586 distance: 116 - 117: 18.122 distance: 117 - 118: 15.265 distance: 117 - 120: 19.714 distance: 118 - 119: 23.852 distance: 121 - 122: 17.301 distance: 122 - 123: 9.742 distance: 122 - 125: 20.541 distance: 123 - 124: 8.590 distance: 123 - 130: 9.083 distance: 125 - 126: 13.862 distance: 126 - 127: 10.238 distance: 127 - 128: 16.666 distance: 128 - 129: 17.421 distance: 130 - 131: 14.559 distance: 131 - 132: 21.973 distance: 131 - 134: 11.407 distance: 132 - 133: 22.396 distance: 132 - 137: 18.376 distance: 134 - 135: 10.417 distance: 134 - 136: 13.580 distance: 137 - 138: 17.066 distance: 138 - 139: 4.065 distance: 138 - 141: 13.695 distance: 139 - 140: 29.990 distance: 139 - 144: 9.275 distance: 141 - 142: 27.717 distance: 141 - 143: 31.874 distance: 144 - 145: 17.333 distance: 145 - 146: 34.431 distance: 145 - 148: 13.170 distance: 146 - 147: 35.741 distance: 146 - 149: 31.798