Starting phenix.real_space_refine on Tue Sep 24 10:19:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u63_41942/09_2024/8u63_41942.cif" } resolution = 3.01 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= 0.014 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 46 5.16 5 C 4894 2.51 5 N 1350 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3836 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 465} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 8.32, per 1000 atoms: 1.07 Number of scatterers: 7758 At special positions: 0 Unit cell: (105.777, 99.207, 106.434, 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 46 16.00 O 1468 8.00 N 1350 7.00 C 4894 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 - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 44.6% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.613A pdb=" N VAL A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.861A pdb=" N GLY A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 294 through 338 removed outlier: 3.881A pdb=" N ALA A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.965A pdb=" N LEU A 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 350 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 4.063A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.863A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.017A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.752A pdb=" N GLU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 415 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 416 " --> pdb=" O GLU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 416' Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.518A pdb=" N GLN A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 removed outlier: 3.833A pdb=" N GLU A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 removed outlier: 3.744A pdb=" N ASN A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.612A pdb=" N VAL B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.861A pdb=" N GLY B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 294 through 338 removed outlier: 3.882A pdb=" N ALA B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.965A pdb=" N LEU B 349 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 350 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 removed outlier: 4.062A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.864A pdb=" N THR B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.018A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.753A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 415 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 416' Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.517A pdb=" N GLN B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 480 removed outlier: 3.834A pdb=" N GLU B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 removed outlier: 3.744A pdb=" N ASN B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 4.133A pdb=" N GLN A 45 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 33 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 93 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 5.571A pdb=" N VAL A 182 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG A 173 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 184 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 273 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU A 282 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 271 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A 284 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET A 269 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A 286 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER A 267 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 3.627A pdb=" N GLN A 240 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 377 Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 4.133A pdb=" N GLN B 45 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 33 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU B 101 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 93 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 5.572A pdb=" N VAL B 182 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG B 173 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 184 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 273 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU B 282 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 271 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 284 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET B 269 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 286 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER B 267 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 235 removed outlier: 3.627A pdb=" N GLN B 240 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 372 through 377 393 hydrogen bonds defined for protein. 1095 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: 2.43 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1437 1.32 - 1.45: 1913 1.45 - 1.57: 4488 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7916 Sorted by residual: bond pdb=" CA VAL A 231 " pdb=" CB VAL A 231 " ideal model delta sigma weight residual 1.538 1.529 0.010 8.80e-03 1.29e+04 1.21e+00 bond pdb=" CB GLN B 64 " pdb=" CG GLN B 64 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.53e-01 bond pdb=" CA VAL B 231 " pdb=" CB VAL B 231 " ideal model delta sigma weight residual 1.538 1.530 0.008 8.80e-03 1.29e+04 9.18e-01 bond pdb=" CB GLN A 64 " pdb=" CG GLN A 64 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.75e-01 bond pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.65e-01 ... (remaining 7911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10570 1.68 - 3.36: 151 3.36 - 5.04: 29 5.04 - 6.72: 4 6.72 - 8.40: 6 Bond angle restraints: 10760 Sorted by residual: angle pdb=" CB MET A 392 " pdb=" CG MET A 392 " pdb=" SD MET A 392 " ideal model delta sigma weight residual 112.70 104.76 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" CB MET B 392 " pdb=" CG MET B 392 " pdb=" SD MET B 392 " ideal model delta sigma weight residual 112.70 104.76 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" CB MET A 338 " pdb=" CG MET A 338 " pdb=" SD MET A 338 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.19e+00 angle pdb=" CB MET B 338 " pdb=" CG MET B 338 " pdb=" SD MET B 338 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.18e+00 angle pdb=" CA MET A 392 " pdb=" CB MET A 392 " pdb=" CG MET A 392 " ideal model delta sigma weight residual 114.10 119.07 -4.97 2.00e+00 2.50e-01 6.17e+00 ... (remaining 10755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4100 17.73 - 35.46: 510 35.46 - 53.19: 130 53.19 - 70.92: 44 70.92 - 88.65: 18 Dihedral angle restraints: 4802 sinusoidal: 1954 harmonic: 2848 Sorted by residual: dihedral pdb=" CA ARG A 324 " pdb=" C ARG A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ARG B 324 " pdb=" C ARG B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta harmonic sigma weight residual 180.00 164.06 15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CG ARG B 386 " pdb=" CD ARG B 386 " pdb=" NE ARG B 386 " pdb=" CZ ARG B 386 " ideal model delta sinusoidal sigma weight residual 90.00 133.59 -43.59 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 4799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 715 0.027 - 0.054: 298 0.054 - 0.081: 106 0.081 - 0.108: 67 0.108 - 0.135: 22 Chirality restraints: 1208 Sorted by residual: chirality pdb=" CA ILE B 220 " pdb=" N ILE B 220 " pdb=" C ILE B 220 " pdb=" CB ILE B 220 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 220 " pdb=" N ILE A 220 " pdb=" C ILE A 220 " pdb=" CB ILE A 220 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL B 53 " pdb=" N VAL B 53 " pdb=" C VAL B 53 " pdb=" CB VAL B 53 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 1205 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 231 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 232 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 232 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 289 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 290 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.019 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 178 2.70 - 3.25: 7408 3.25 - 3.80: 12140 3.80 - 4.35: 15907 4.35 - 4.90: 26649 Nonbonded interactions: 62282 Sorted by model distance: nonbonded pdb=" OG1 THR A 65 " pdb=" OD1 ASP A 67 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OD1 ASP B 67 " model vdw 2.152 3.040 nonbonded pdb=" O SER A 309 " pdb=" OG SER A 313 " model vdw 2.252 3.040 nonbonded pdb=" O SER B 309 " pdb=" OG SER B 313 " model vdw 2.253 3.040 nonbonded pdb=" O GLY A 305 " pdb=" OG SER A 309 " model vdw 2.276 3.040 ... (remaining 62277 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' selection = chain 'B' } 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: 10.690 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 0.040 7916 Z= 0.183 Angle : 0.559 8.401 10760 Z= 0.278 Chirality : 0.041 0.135 1208 Planarity : 0.004 0.046 1402 Dihedral : 17.941 88.648 2954 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.48 % Allowed : 27.62 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.74 (0.25), residues: 972 helix: -0.09 (0.24), residues: 400 sheet: -0.28 (0.36), residues: 164 loop : -0.84 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 280 HIS 0.011 0.001 HIS A 295 PHE 0.009 0.001 PHE A 199 TYR 0.023 0.002 TYR B 225 ARG 0.007 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8300 (p) cc_final: 0.8075 (p) REVERT: A 333 GLN cc_start: 0.7942 (tt0) cc_final: 0.7671 (tt0) REVERT: A 480 MET cc_start: 0.8073 (mmm) cc_final: 0.7658 (tpp) REVERT: B 79 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7483 (mmt-90) REVERT: B 372 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 435 VAL cc_start: 0.8460 (m) cc_final: 0.8117 (p) outliers start: 4 outliers final: 1 residues processed: 197 average time/residue: 0.2632 time to fit residues: 65.1987 Evaluate side-chains 189 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 306 GLN A 433 ASN B 262 ASN B 302 GLN B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7916 Z= 0.225 Angle : 0.576 8.476 10760 Z= 0.285 Chirality : 0.042 0.141 1208 Planarity : 0.005 0.041 1402 Dihedral : 5.819 55.617 1104 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.38 % Allowed : 24.64 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.23 (0.26), residues: 972 helix: 1.03 (0.25), residues: 408 sheet: 0.28 (0.37), residues: 160 loop : -0.74 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 280 HIS 0.010 0.002 HIS A 295 PHE 0.012 0.002 PHE A 199 TYR 0.009 0.001 TYR A 400 ARG 0.007 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 96 SER cc_start: 0.8559 (m) cc_final: 0.8293 (t) REVERT: A 154 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 164 THR cc_start: 0.8416 (p) cc_final: 0.8167 (p) REVERT: A 167 ASP cc_start: 0.8154 (m-30) cc_final: 0.7841 (m-30) REVERT: A 206 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7162 (tp30) REVERT: A 308 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 319 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6808 (tm-30) REVERT: B 64 GLN cc_start: 0.6818 (mp10) cc_final: 0.6534 (mp10) REVERT: B 94 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 139 MET cc_start: 0.7180 (mtm) cc_final: 0.6814 (mtm) REVERT: B 337 MET cc_start: 0.7538 (mpm) cc_final: 0.7331 (mpm) outliers start: 20 outliers final: 7 residues processed: 214 average time/residue: 0.2522 time to fit residues: 68.4824 Evaluate side-chains 203 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 369 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 351 GLN A 433 ASN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7916 Z= 0.374 Angle : 0.625 9.884 10760 Z= 0.306 Chirality : 0.045 0.150 1208 Planarity : 0.005 0.047 1402 Dihedral : 5.815 52.609 1102 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.05 % Allowed : 23.57 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.37 (0.26), residues: 972 helix: 1.24 (0.25), residues: 406 sheet: 0.35 (0.37), residues: 162 loop : -0.79 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 437 HIS 0.010 0.002 HIS B 295 PHE 0.014 0.002 PHE A 34 TYR 0.008 0.002 TYR A 415 ARG 0.012 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8713 (m) cc_final: 0.8400 (t) REVERT: A 154 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 163 MET cc_start: 0.8011 (mtp) cc_final: 0.7723 (ttm) REVERT: A 164 THR cc_start: 0.8449 (p) cc_final: 0.8242 (p) REVERT: A 304 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 319 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6872 (tm-30) REVERT: A 337 MET cc_start: 0.6784 (mpm) cc_final: 0.6514 (mpm) REVERT: B 94 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 139 MET cc_start: 0.7189 (mtm) cc_final: 0.6888 (mtm) REVERT: B 275 GLN cc_start: 0.8057 (pp30) cc_final: 0.7576 (pt0) REVERT: B 316 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7078 (mt-10) REVERT: B 324 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7854 (ptm160) REVERT: B 435 VAL cc_start: 0.8487 (m) cc_final: 0.8279 (p) outliers start: 34 outliers final: 19 residues processed: 226 average time/residue: 0.2295 time to fit residues: 66.8183 Evaluate side-chains 217 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 408 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN A 306 GLN A 433 ASN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 262 ASN B 306 GLN B 389 HIS B 433 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7916 Z= 0.200 Angle : 0.549 8.620 10760 Z= 0.270 Chirality : 0.042 0.138 1208 Planarity : 0.005 0.055 1402 Dihedral : 5.700 56.016 1102 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.86 % Allowed : 26.43 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.66 (0.27), residues: 972 helix: 1.53 (0.26), residues: 406 sheet: 0.46 (0.38), residues: 160 loop : -0.66 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 391 HIS 0.007 0.001 HIS B 295 PHE 0.010 0.001 PHE A 34 TYR 0.008 0.001 TYR B 172 ARG 0.007 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8641 (m) cc_final: 0.8359 (t) REVERT: A 154 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6958 (mt-10) REVERT: A 163 MET cc_start: 0.7998 (mtp) cc_final: 0.7720 (ttm) REVERT: A 164 THR cc_start: 0.8437 (p) cc_final: 0.8226 (p) REVERT: A 167 ASP cc_start: 0.8116 (m-30) cc_final: 0.7863 (m-30) REVERT: A 246 PHE cc_start: 0.8877 (m-80) cc_final: 0.8641 (m-80) REVERT: A 304 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8242 (mt) REVERT: A 319 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6897 (tm-30) REVERT: A 336 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: A 337 MET cc_start: 0.6804 (mpm) cc_final: 0.6531 (mpm) REVERT: B 139 MET cc_start: 0.7140 (mtm) cc_final: 0.6797 (mtm) REVERT: B 273 LEU cc_start: 0.8546 (mt) cc_final: 0.8286 (mp) outliers start: 24 outliers final: 13 residues processed: 211 average time/residue: 0.2495 time to fit residues: 66.9120 Evaluate side-chains 205 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 408 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 351 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7916 Z= 0.295 Angle : 0.583 10.262 10760 Z= 0.285 Chirality : 0.043 0.164 1208 Planarity : 0.005 0.051 1402 Dihedral : 5.745 54.194 1102 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.62 % Allowed : 27.14 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.73 (0.27), residues: 972 helix: 1.59 (0.26), residues: 408 sheet: 0.49 (0.39), residues: 160 loop : -0.63 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 280 HIS 0.008 0.001 HIS B 295 PHE 0.012 0.002 PHE A 34 TYR 0.008 0.001 TYR B 172 ARG 0.008 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.7303 (mp10) cc_final: 0.7026 (mp10) REVERT: A 96 SER cc_start: 0.8694 (m) cc_final: 0.8407 (t) REVERT: A 154 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 163 MET cc_start: 0.8048 (mtp) cc_final: 0.7756 (ttm) REVERT: A 167 ASP cc_start: 0.8098 (m-30) cc_final: 0.7791 (m-30) REVERT: A 246 PHE cc_start: 0.8866 (m-80) cc_final: 0.8659 (m-80) REVERT: A 319 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6927 (tm-30) REVERT: A 336 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: A 337 MET cc_start: 0.6843 (mpm) cc_final: 0.6610 (mpm) REVERT: B 94 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 139 MET cc_start: 0.7118 (mtm) cc_final: 0.6814 (mtm) REVERT: B 158 ARG cc_start: 0.7440 (tpm170) cc_final: 0.7211 (tpm170) REVERT: B 266 LEU cc_start: 0.8709 (mt) cc_final: 0.8503 (mt) REVERT: B 435 VAL cc_start: 0.8460 (m) cc_final: 0.8247 (p) outliers start: 22 outliers final: 17 residues processed: 215 average time/residue: 0.2321 time to fit residues: 64.3979 Evaluate side-chains 215 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 408 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7916 Z= 0.245 Angle : 0.569 9.427 10760 Z= 0.278 Chirality : 0.042 0.137 1208 Planarity : 0.005 0.052 1402 Dihedral : 5.729 55.187 1102 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.45 % Allowed : 26.79 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.86 (0.27), residues: 972 helix: 1.75 (0.25), residues: 406 sheet: 0.49 (0.39), residues: 160 loop : -0.58 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 391 HIS 0.007 0.001 HIS B 295 PHE 0.011 0.002 PHE B 34 TYR 0.008 0.001 TYR B 172 ARG 0.007 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8687 (m) cc_final: 0.8407 (t) REVERT: A 154 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 163 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7778 (ttm) REVERT: A 167 ASP cc_start: 0.8083 (m-30) cc_final: 0.7759 (m-30) REVERT: A 319 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6936 (tm-30) REVERT: A 336 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: A 337 MET cc_start: 0.6856 (mpm) cc_final: 0.6618 (mpm) REVERT: B 94 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 139 MET cc_start: 0.7130 (mtm) cc_final: 0.6825 (mtm) REVERT: B 266 LEU cc_start: 0.8691 (mt) cc_final: 0.8480 (mt) REVERT: B 435 VAL cc_start: 0.8446 (m) cc_final: 0.8225 (p) outliers start: 29 outliers final: 21 residues processed: 219 average time/residue: 0.2493 time to fit residues: 69.4357 Evaluate side-chains 218 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 69 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7916 Z= 0.219 Angle : 0.558 9.956 10760 Z= 0.273 Chirality : 0.042 0.141 1208 Planarity : 0.005 0.056 1402 Dihedral : 5.700 55.895 1102 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.98 % Allowed : 27.38 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.96 (0.27), residues: 972 helix: 1.86 (0.26), residues: 406 sheet: 0.49 (0.39), residues: 160 loop : -0.53 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 391 HIS 0.009 0.001 HIS B 295 PHE 0.011 0.001 PHE B 34 TYR 0.008 0.001 TYR B 172 ARG 0.007 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8666 (m) cc_final: 0.8401 (t) REVERT: A 154 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6840 (mt-10) REVERT: A 163 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7772 (ttm) REVERT: A 167 ASP cc_start: 0.8064 (m-30) cc_final: 0.7740 (m-30) REVERT: A 319 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6952 (tm-30) REVERT: A 324 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7019 (ttm170) REVERT: A 337 MET cc_start: 0.6867 (mpm) cc_final: 0.6643 (mpm) REVERT: B 94 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 139 MET cc_start: 0.7122 (mtm) cc_final: 0.6827 (mtm) REVERT: B 158 ARG cc_start: 0.7397 (tpm170) cc_final: 0.7152 (tpm170) REVERT: B 273 LEU cc_start: 0.8543 (mt) cc_final: 0.8276 (mp) REVERT: B 435 VAL cc_start: 0.8426 (m) cc_final: 0.8218 (p) outliers start: 25 outliers final: 21 residues processed: 218 average time/residue: 0.2620 time to fit residues: 72.5846 Evaluate side-chains 218 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7916 Z= 0.229 Angle : 0.562 9.810 10760 Z= 0.275 Chirality : 0.042 0.142 1208 Planarity : 0.005 0.040 1402 Dihedral : 5.693 56.000 1102 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.69 % Allowed : 26.90 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.01 (0.27), residues: 972 helix: 1.89 (0.26), residues: 408 sheet: 0.49 (0.39), residues: 160 loop : -0.48 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 391 HIS 0.010 0.001 HIS B 295 PHE 0.010 0.001 PHE A 199 TYR 0.008 0.001 TYR B 172 ARG 0.010 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8689 (m) cc_final: 0.8414 (t) REVERT: A 154 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 163 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7775 (ttm) REVERT: A 167 ASP cc_start: 0.8076 (m-30) cc_final: 0.7717 (m-30) REVERT: A 324 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7003 (ttm170) REVERT: A 337 MET cc_start: 0.6862 (mpm) cc_final: 0.6641 (mpm) REVERT: B 94 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 139 MET cc_start: 0.7111 (mtm) cc_final: 0.6829 (mtm) REVERT: B 158 ARG cc_start: 0.7386 (tpm170) cc_final: 0.7145 (tpm170) REVERT: B 273 LEU cc_start: 0.8542 (mt) cc_final: 0.8275 (mp) REVERT: B 435 VAL cc_start: 0.8425 (m) cc_final: 0.8221 (p) outliers start: 31 outliers final: 24 residues processed: 215 average time/residue: 0.2358 time to fit residues: 65.4192 Evaluate side-chains 223 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7916 Z= 0.225 Angle : 0.563 9.424 10760 Z= 0.275 Chirality : 0.042 0.148 1208 Planarity : 0.005 0.040 1402 Dihedral : 5.687 56.053 1102 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.45 % Allowed : 27.02 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.04 (0.27), residues: 972 helix: 1.93 (0.26), residues: 408 sheet: 0.34 (0.38), residues: 170 loop : -0.42 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 391 HIS 0.010 0.001 HIS B 295 PHE 0.010 0.001 PHE A 199 TYR 0.008 0.001 TYR B 172 ARG 0.007 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8674 (m) cc_final: 0.8405 (t) REVERT: A 139 MET cc_start: 0.7191 (mtm) cc_final: 0.6347 (mtm) REVERT: A 154 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6826 (mt-10) REVERT: A 163 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7829 (ttm) REVERT: A 167 ASP cc_start: 0.8076 (m-30) cc_final: 0.7723 (m-30) REVERT: A 324 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6981 (ttm170) REVERT: B 79 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7796 (mtt-85) REVERT: B 94 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 139 MET cc_start: 0.7103 (mtm) cc_final: 0.6830 (mtm) REVERT: B 158 ARG cc_start: 0.7395 (tpm170) cc_final: 0.7151 (tpm170) REVERT: B 273 LEU cc_start: 0.8540 (mt) cc_final: 0.8274 (mp) REVERT: B 275 GLN cc_start: 0.8015 (pp30) cc_final: 0.7624 (pt0) outliers start: 29 outliers final: 26 residues processed: 214 average time/residue: 0.2401 time to fit residues: 65.3800 Evaluate side-chains 220 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 72.6579 > 50: distance: 34 - 120: 27.157 distance: 37 - 117: 32.502 distance: 107 - 111: 33.760 distance: 111 - 112: 40.046 distance: 112 - 113: 58.404 distance: 112 - 115: 56.482 distance: 113 - 114: 50.707 distance: 113 - 117: 66.026 distance: 115 - 116: 49.366 distance: 117 - 118: 57.536 distance: 118 - 119: 56.746 distance: 119 - 120: 22.538 distance: 119 - 121: 53.326 distance: 121 - 122: 17.407 distance: 122 - 123: 25.109 distance: 122 - 125: 8.870 distance: 123 - 124: 26.239 distance: 123 - 131: 47.219 distance: 125 - 126: 51.426 distance: 126 - 127: 31.083 distance: 126 - 128: 34.834 distance: 127 - 129: 6.877 distance: 128 - 130: 18.863 distance: 129 - 130: 7.049 distance: 131 - 132: 36.459 distance: 132 - 133: 48.772 distance: 132 - 135: 9.913 distance: 133 - 134: 8.247 distance: 133 - 142: 59.559 distance: 135 - 136: 33.467 distance: 136 - 137: 20.260 distance: 137 - 138: 31.977 distance: 138 - 139: 25.833 distance: 139 - 140: 7.649 distance: 139 - 141: 14.660 distance: 142 - 143: 51.557 distance: 143 - 144: 40.287 distance: 143 - 146: 41.666 distance: 144 - 145: 55.833 distance: 144 - 149: 69.207 distance: 146 - 147: 56.777 distance: 146 - 148: 50.434 distance: 149 - 150: 64.835 distance: 149 - 155: 56.240 distance: 150 - 151: 60.006 distance: 150 - 153: 41.712 distance: 151 - 152: 49.039 distance: 151 - 156: 57.552 distance: 153 - 154: 45.646 distance: 154 - 155: 56.502 distance: 156 - 157: 14.792 distance: 157 - 158: 16.008 distance: 157 - 160: 56.718 distance: 158 - 159: 49.804 distance: 158 - 164: 46.583 distance: 160 - 161: 38.838 distance: 161 - 162: 22.237 distance: 161 - 163: 40.420 distance: 164 - 165: 24.700 distance: 165 - 166: 25.525 distance: 165 - 168: 56.593 distance: 166 - 167: 22.436 distance: 166 - 176: 61.473 distance: 168 - 169: 35.132 distance: 169 - 170: 30.301 distance: 169 - 171: 25.131 distance: 170 - 172: 43.098 distance: 171 - 173: 31.620 distance: 172 - 174: 42.095 distance: 173 - 174: 23.272 distance: 174 - 175: 38.418 distance: 176 - 177: 55.250 distance: 177 - 178: 56.713 distance: 177 - 180: 68.600 distance: 178 - 179: 58.254 distance: 180 - 181: 55.649 distance: 180 - 182: 44.414 distance: 183 - 184: 33.507 distance: 184 - 185: 31.014 distance: 184 - 187: 50.438 distance: 185 - 186: 59.165 distance: 185 - 189: 35.489 distance: 186 - 207: 27.817 distance: 187 - 188: 56.095