Starting phenix.real_space_refine on Sun Oct 13 12:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/10_2024/8sd3_40349.cif" } resolution = 2.95 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= 0.006 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 8 5.49 5 S 36 5.16 5 C 5276 2.51 5 N 1156 2.21 5 O 1352 1.98 5 H 6824 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 122 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 13.12, per 1000 atoms: 0.90 Number of scatterers: 14656 At special positions: 0 Unit cell: (107.06, 107.06, 69.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 36 16.00 P 8 15.00 O 1352 8.00 N 1156 7.00 C 5276 6.00 H 6824 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 - 3.00 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: 4.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 87.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 4.261A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.838A pdb=" N ARG A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.948A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.261A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.837A pdb=" N ARG B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 306 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 350 Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.147A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.949A pdb=" N ILE B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.521A pdb=" N TYR C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 removed outlier: 4.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.837A pdb=" N ARG C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 306 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 350 Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.760A pdb=" N ILE C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 428 removed outlier: 3.949A pdb=" N ILE C 408 " --> pdb=" O PRO C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.968A pdb=" N VAL D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.004A pdb=" N LYS D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.520A pdb=" N TYR D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 4.262A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 removed outlier: 3.838A pdb=" N ARG D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 306 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.730A pdb=" N GLN D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 350 Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.146A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.759A pdb=" N ILE D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.948A pdb=" N ILE D 408 " --> pdb=" O PRO D 404 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1632 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: 5.23 Time building geometry restraints manager: 4.82 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: 6812 1.03 - 1.22: 52 1.22 - 1.42: 3044 1.42 - 1.61: 4820 1.61 - 1.81: 68 Bond restraints: 14796 Sorted by residual: bond pdb=" C21 POV B1004 " pdb=" O21 POV B1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV C1004 " pdb=" O21 POV C1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV D1004 " pdb=" O21 POV D1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1004 " pdb=" O21 POV A1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1003 " pdb=" O21 POV A1003 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 14791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 25755 2.07 - 4.14: 339 4.14 - 6.21: 126 6.21 - 8.28: 44 8.28 - 10.35: 36 Bond angle restraints: 26300 Sorted by residual: angle pdb=" C32 POV B1002 " pdb=" C31 POV B1002 " pdb=" O31 POV B1002 " ideal model delta sigma weight residual 110.66 121.01 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C32 POV A1002 " pdb=" C31 POV A1002 " pdb=" O31 POV A1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV D1002 " pdb=" C31 POV D1002 " pdb=" O31 POV D1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1002 " pdb=" C31 POV C1002 " pdb=" O31 POV C1002 " ideal model delta sigma weight residual 110.66 120.95 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1003 " pdb=" C31 POV C1003 " pdb=" O31 POV C1003 " ideal model delta sigma weight residual 110.66 120.68 -10.02 3.00e+00 1.11e-01 1.12e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 6696 21.11 - 42.22: 320 42.22 - 63.32: 164 63.32 - 84.43: 24 84.43 - 105.54: 16 Dihedral angle restraints: 7220 sinusoidal: 3912 harmonic: 3308 Sorted by residual: dihedral pdb=" C3 POV D1001 " pdb=" C31 POV D1001 " pdb=" O31 POV D1001 " pdb=" C32 POV D1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.85 -105.54 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV A1001 " pdb=" C31 POV A1001 " pdb=" O31 POV A1001 " pdb=" C32 POV A1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.87 -105.52 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV C1001 " pdb=" C31 POV C1001 " pdb=" O31 POV C1001 " pdb=" C32 POV C1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.89 -105.50 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1110 0.067 - 0.134: 147 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 4 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CG LEU D 207 " pdb=" CB LEU D 207 " pdb=" CD1 LEU D 207 " pdb=" CD2 LEU D 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU A 207 " pdb=" CB LEU A 207 " pdb=" CD1 LEU A 207 " pdb=" CD2 LEU A 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU B 207 " pdb=" CB LEU B 207 " pdb=" CD1 LEU B 207 " pdb=" CD2 LEU B 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1261 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE B 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE B 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE B 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE B 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE A 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 254 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 254 " 0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE C 254 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE C 254 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 254 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE C 254 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 254 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 254 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE C 254 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE C 254 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE C 254 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 254 " 0.013 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.47: 8394 2.47 - 3.14: 39699 3.14 - 3.81: 49736 3.81 - 4.47: 74365 4.47 - 5.14: 112037 Nonbonded interactions: 284231 Sorted by model distance: nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ASP D 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS A 356 " pdb=" O ASP A 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS B 356 " pdb=" O ASP B 378 " model vdw 1.808 2.450 nonbonded pdb=" HZ3 LYS C 356 " pdb=" O ASP C 378 " model vdw 1.808 2.450 nonbonded pdb=" O THR A 372 " pdb=" HG1 THR A 373 " model vdw 1.813 2.450 ... (remaining 284226 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'B' and (resid 171 through 428 or resid 1000 through 1001 or (resid 1002 \ and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name O21 or name O22 or name O31 or name O32)) \ or (resid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name O21 or name O22) \ ) or (resid 1004 through 1005 and (name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name O22)))) selection = (chain 'C' and (resid 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'D' and (resid 171 through 428 or resid 1000 through 1001 or (resid 1002 \ and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name O21 or name O22 or name O31 or name O32)) \ or (resid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name O21 or name O22) \ ) or (resid 1004 through 1005 and (name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name O22)))) } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.740 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.010 0.128 7972 Z= 0.631 Angle : 1.079 10.351 10752 Z= 0.445 Chirality : 0.045 0.335 1264 Planarity : 0.005 0.047 1264 Dihedral : 16.417 105.541 2952 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.86 (0.28), residues: 924 helix: 1.53 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.27 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 365 HIS 0.001 0.000 HIS B 227 PHE 0.085 0.003 PHE B 254 TYR 0.009 0.002 TYR A 376 ARG 0.004 0.001 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 2.0656 time to fit residues: 248.9853 Evaluate side-chains 100 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 205 ASN B 179 ASN B 205 ASN C 179 ASN D 179 ASN D 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7972 Z= 0.169 Angle : 0.516 4.215 10752 Z= 0.261 Chirality : 0.036 0.114 1264 Planarity : 0.005 0.048 1264 Dihedral : 15.248 83.390 1328 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.55 % Allowed : 7.25 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.29), residues: 924 helix: 2.02 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.12 (0.52), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 365 HIS 0.001 0.000 HIS D 309 PHE 0.015 0.001 PHE B 244 TYR 0.003 0.001 TYR D 416 ARG 0.003 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.201 Fit side-chains REVERT: A 356 LYS cc_start: 0.8963 (mttt) cc_final: 0.8722 (mttm) REVERT: A 378 ASP cc_start: 0.8933 (p0) cc_final: 0.8712 (p0) REVERT: B 356 LYS cc_start: 0.8959 (mttt) cc_final: 0.8728 (mttm) REVERT: B 378 ASP cc_start: 0.8940 (p0) cc_final: 0.8697 (p0) REVERT: C 356 LYS cc_start: 0.9027 (mttt) cc_final: 0.8767 (mttm) REVERT: C 378 ASP cc_start: 0.8904 (p0) cc_final: 0.8680 (p0) REVERT: D 356 LYS cc_start: 0.9005 (mttt) cc_final: 0.8756 (mttm) REVERT: D 378 ASP cc_start: 0.8939 (p0) cc_final: 0.8680 (OUTLIER) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 2.0616 time to fit residues: 295.9398 Evaluate side-chains 117 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1790 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: