Starting phenix.real_space_refine on Mon Mar 11 11:13:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irl_35678/03_2024/8irl_35678.pdb" } resolution = 2.7 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= 0.004 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 52 5.16 5 C 5280 2.51 5 N 1306 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.02, per 1000 atoms: 0.62 Number of scatterers: 8108 At special positions: 0 Unit cell: (97.865, 108.077, 102.12, 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 52 16.00 O 1470 8.00 N 1306 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 67.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.284A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 150 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.508A pdb=" N ILE A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.913A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.883A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.960A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 375' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.942A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.013A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 484 through 496 removed outlier: 4.083A pdb=" N LEU A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.714A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 3.918A pdb=" N GLY A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.289A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 150 Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.503A pdb=" N ILE B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.902A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 330 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.869A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.954A pdb=" N ILE B 374 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.988A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 450 removed outlier: 4.007A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 484 through 496 removed outlier: 4.088A pdb=" N LEU B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.680A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 554 removed outlier: 3.926A pdb=" N GLY B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 244 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 275 removed outlier: 11.871A pdb=" N ARG A 259 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 267 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR A 267 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 11.838A pdb=" N ARG B 259 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 removed outlier: 11.871A pdb=" N ARG A 259 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 267 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR A 267 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 11.838A pdb=" N ARG B 259 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA6, first strand: chain 'B' and resid 241 through 244 504 hydrogen bonds defined for protein. 1440 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: 2.44 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1258 1.31 - 1.44: 2228 1.44 - 1.57: 4722 1.57 - 1.69: 2 1.69 - 1.82: 84 Bond restraints: 8294 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.537 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.532 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.529 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.529 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 227 106.41 - 113.31: 4605 113.31 - 120.20: 3024 120.20 - 127.10: 3354 127.10 - 134.00: 80 Bond angle restraints: 11290 Sorted by residual: angle pdb=" C GLY A 485 " pdb=" N PRO A 486 " pdb=" CA PRO A 486 " ideal model delta sigma weight residual 120.38 114.94 5.44 1.03e+00 9.43e-01 2.79e+01 angle pdb=" C GLY B 485 " pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta sigma weight residual 120.38 114.96 5.42 1.03e+00 9.43e-01 2.77e+01 angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 112.34 120.25 -7.91 2.04e+00 2.40e-01 1.50e+01 angle pdb=" N GLY A 485 " pdb=" CA GLY A 485 " pdb=" C GLY A 485 " ideal model delta sigma weight residual 112.34 120.12 -7.78 2.04e+00 2.40e-01 1.46e+01 angle pdb=" C THR B 247 " pdb=" N LEU B 248 " pdb=" CA LEU B 248 " ideal model delta sigma weight residual 121.54 128.61 -7.07 1.91e+00 2.74e-01 1.37e+01 ... (remaining 11285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 4680 23.67 - 47.34: 192 47.34 - 71.01: 16 71.01 - 94.68: 5 94.68 - 118.35: 3 Dihedral angle restraints: 4896 sinusoidal: 1844 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 254 " pdb=" SG CYS B 254 " pdb=" SG CYS B 287 " pdb=" CB CYS B 287 " ideal model delta sinusoidal sigma weight residual 93.00 162.44 -69.44 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS A 254 " pdb=" SG CYS A 254 " pdb=" SG CYS A 287 " pdb=" CB CYS A 287 " ideal model delta sinusoidal sigma weight residual 93.00 162.41 -69.41 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CA ASN A 235 " pdb=" C ASN A 235 " pdb=" N GLN A 236 " pdb=" CA GLN A 236 " ideal model delta harmonic sigma weight residual 180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1051 0.050 - 0.101: 254 0.101 - 0.151: 46 0.151 - 0.201: 1 0.201 - 0.252: 4 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C6 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.66 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C5 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C6 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.62 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1353 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 248 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU A 248 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU A 248 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL A 249 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 248 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU B 248 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU B 248 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL B 249 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO A 487 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.037 5.00e-02 4.00e+02 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 31 2.59 - 3.17: 7024 3.17 - 3.75: 12140 3.75 - 4.32: 16886 4.32 - 4.90: 28488 Nonbonded interactions: 64569 Sorted by model distance: nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.014 2.440 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.094 2.440 nonbonded pdb=" OG SER B 268 " pdb=" OD1 ASN B 270 " model vdw 2.131 2.440 nonbonded pdb=" OD1 ASN A 163 " pdb=" OG SER A 437 " model vdw 2.142 2.440 nonbonded pdb=" OD1 ASN B 163 " pdb=" OG SER B 437 " model vdw 2.142 2.440 ... (remaining 64564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.590 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: 3.400 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.260 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 8294 Z= 0.466 Angle : 0.676 7.914 11290 Z= 0.370 Chirality : 0.045 0.252 1356 Planarity : 0.006 0.066 1396 Dihedral : 12.790 118.352 2932 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.48 (0.25), residues: 1076 helix: 1.07 (0.21), residues: 640 sheet: -4.16 (0.76), residues: 20 loop : -0.55 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 380 HIS 0.004 0.001 HIS B 174 PHE 0.021 0.002 PHE B 229 TYR 0.021 0.002 TYR B 309 ARG 0.003 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.953 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.1676 time to fit residues: 104.7589 Evaluate side-chains 73 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8294 Z= 0.159 Angle : 0.525 7.299 11290 Z= 0.281 Chirality : 0.040 0.153 1356 Planarity : 0.005 0.061 1396 Dihedral : 7.056 108.979 1230 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.70 % Allowed : 6.41 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1076 helix: 2.15 (0.21), residues: 632 sheet: -4.09 (0.78), residues: 20 loop : -0.34 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.002 0.001 HIS B 541 PHE 0.012 0.001 PHE A 386 TYR 0.011 0.001 TYR B 418 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.807 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 1.1546 time to fit residues: 92.7143 Evaluate side-chains 71 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.188 Angle : 0.522 7.669 11290 Z= 0.278 Chirality : 0.040 0.148 1356 Planarity : 0.004 0.053 1396 Dihedral : 6.873 108.170 1230 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 8.74 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.70 (0.26), residues: 1076 helix: 2.28 (0.21), residues: 642 sheet: -3.95 (0.80), residues: 20 loop : -0.46 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.002 0.001 HIS B 541 PHE 0.014 0.001 PHE B 166 TYR 0.013 0.001 TYR B 388 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.990 Fit side-chains REVERT: A 207 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8217 (tt) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 1.1030 time to fit residues: 86.5272 Evaluate side-chains 75 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.179 Angle : 0.509 7.852 11290 Z= 0.271 Chirality : 0.040 0.147 1356 Planarity : 0.004 0.049 1396 Dihedral : 6.735 107.209 1230 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.05 % Allowed : 10.26 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.82 (0.26), residues: 1076 helix: 2.41 (0.21), residues: 642 sheet: -3.94 (0.80), residues: 20 loop : -0.46 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 PHE 0.014 0.001 PHE A 166 TYR 0.010 0.001 TYR B 418 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.849 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 1.2360 time to fit residues: 97.5779 Evaluate side-chains 70 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8294 Z= 0.330 Angle : 0.600 8.259 11290 Z= 0.323 Chirality : 0.044 0.152 1356 Planarity : 0.005 0.046 1396 Dihedral : 6.833 105.741 1230 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.17 % Allowed : 11.89 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.56 (0.26), residues: 1076 helix: 2.21 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -0.81 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 380 HIS 0.003 0.001 HIS A 174 PHE 0.016 0.002 PHE A 166 TYR 0.020 0.002 TYR B 388 ARG 0.003 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.942 Fit side-chains REVERT: A 20 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6441 (tt) REVERT: A 207 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8244 (tt) REVERT: B 207 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8183 (tp) outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 1.0763 time to fit residues: 93.7386 Evaluate side-chains 81 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 25 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8294 Z= 0.182 Angle : 0.510 8.038 11290 Z= 0.272 Chirality : 0.040 0.146 1356 Planarity : 0.004 0.044 1396 Dihedral : 6.669 106.146 1230 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 12.24 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.77 (0.26), residues: 1076 helix: 2.39 (0.21), residues: 644 sheet: -3.98 (0.77), residues: 20 loop : -0.55 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 PHE 0.014 0.001 PHE B 166 TYR 0.010 0.001 TYR B 418 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.941 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 76 average time/residue: 1.1921 time to fit residues: 96.8718 Evaluate side-chains 76 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.173 Angle : 0.513 8.114 11290 Z= 0.270 Chirality : 0.040 0.146 1356 Planarity : 0.004 0.044 1396 Dihedral : 6.579 105.670 1230 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.17 % Allowed : 12.70 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.92 (0.26), residues: 1076 helix: 2.51 (0.21), residues: 644 sheet: -3.92 (0.78), residues: 20 loop : -0.48 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.002 0.001 HIS B 541 PHE 0.014 0.001 PHE A 166 TYR 0.022 0.001 TYR A 388 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.966 Fit side-chains REVERT: A 524 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 207 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8169 (tp) REVERT: B 524 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8806 (t80) outliers start: 10 outliers final: 3 residues processed: 74 average time/residue: 1.1222 time to fit residues: 89.1391 Evaluate side-chains 72 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 524 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8294 Z= 0.155 Angle : 0.499 8.066 11290 Z= 0.262 Chirality : 0.039 0.145 1356 Planarity : 0.004 0.043 1396 Dihedral : 6.504 105.501 1230 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.63 % Allowed : 12.82 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.04 (0.26), residues: 1076 helix: 2.59 (0.21), residues: 644 sheet: -3.90 (0.79), residues: 20 loop : -0.39 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.002 0.000 HIS A 541 PHE 0.014 0.001 PHE A 166 TYR 0.009 0.001 TYR A 418 ARG 0.001 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 524 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8768 (t80) REVERT: B 207 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 524 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8769 (t80) outliers start: 14 outliers final: 3 residues processed: 82 average time/residue: 1.2143 time to fit residues: 106.2616 Evaluate side-chains 79 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 524 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.0870 chunk 99 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8294 Z= 0.127 Angle : 0.476 8.229 11290 Z= 0.248 Chirality : 0.038 0.142 1356 Planarity : 0.004 0.043 1396 Dihedral : 6.361 104.591 1230 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.82 % Allowed : 13.87 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.22 (0.26), residues: 1076 helix: 2.71 (0.21), residues: 644 sheet: -3.77 (0.83), residues: 20 loop : -0.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 482 HIS 0.001 0.000 HIS A 541 PHE 0.013 0.001 PHE A 166 TYR 0.026 0.001 TYR A 388 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.7514 (mm) cc_final: 0.7277 (mp) REVERT: A 524 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8710 (t80) REVERT: B 468 LEU cc_start: 0.7547 (mm) cc_final: 0.7324 (mp) REVERT: B 524 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8721 (t80) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 1.2534 time to fit residues: 104.6145 Evaluate side-chains 81 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 524 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8294 Z= 0.133 Angle : 0.481 8.317 11290 Z= 0.250 Chirality : 0.039 0.141 1356 Planarity : 0.004 0.043 1396 Dihedral : 6.274 103.575 1230 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.82 % Allowed : 13.87 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.28 (0.26), residues: 1076 helix: 2.74 (0.21), residues: 644 sheet: -3.83 (0.81), residues: 20 loop : -0.22 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS A 541 PHE 0.013 0.001 PHE B 166 TYR 0.008 0.001 TYR A 418 ARG 0.002 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.936 Fit side-chains REVERT: A 103 ARG cc_start: 0.6750 (pmt170) cc_final: 0.6543 (pmt170) REVERT: A 468 LEU cc_start: 0.7562 (mm) cc_final: 0.7330 (mp) REVERT: A 524 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8737 (t80) REVERT: B 468 LEU cc_start: 0.7618 (mm) cc_final: 0.7386 (mp) REVERT: B 524 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8730 (t80) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 1.2316 time to fit residues: 100.0442 Evaluate side-chains 79 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 524 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088171 restraints weight = 9996.930| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.03 r_work: 0.2863 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8294 Z= 0.217 Angle : 0.540 8.570 11290 Z= 0.284 Chirality : 0.041 0.143 1356 Planarity : 0.004 0.044 1396 Dihedral : 6.356 102.421 1230 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 13.52 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.09 (0.26), residues: 1076 helix: 2.59 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.002 0.001 HIS B 174 PHE 0.015 0.001 PHE A 166 TYR 0.026 0.002 TYR A 388 ARG 0.003 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2573.58 seconds wall clock time: 46 minutes 42.98 seconds (2802.98 seconds total)