Starting phenix.real_space_refine on Mon Nov 18 11:31:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/11_2024/8irp_35682_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 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 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.57, per 1000 atoms: 0.52 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 109.779, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.03 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 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=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.66 Conformation dependent library (CDL) restraints added in 1.6 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 68.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.233A 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 149 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.855A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.618A pdb=" N LEU B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.331A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.243A 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 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.933A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.668A pdb=" N ILE B 374 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.486A 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: 3.687A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 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 480 through 495 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.530A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.834A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 554 removed outlier: 4.619A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.233A 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 149 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.855A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.618A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.332A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.242A 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 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.933A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.668A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.487A 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: 3.687A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.007A 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 480 through 495 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.530A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.833A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.619A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.685A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.819A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 510 hydrogen bonds defined for protein. 1446 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: 6.72 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3412 1.42 - 1.62: 4824 1.62 - 1.81: 84 Bond restraints: 16538 Sorted by residual: bond pdb=" C6 H35 A 701 " pdb=" N6 H35 A 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C6 H35 B 701 " pdb=" N6 H35 B 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CAM H35 B 701 " pdb=" CAO H35 B 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" CAM H35 A 701 " pdb=" CAO H35 A 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 16533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 29627 1.81 - 3.62: 251 3.62 - 5.43: 38 5.43 - 7.24: 4 7.24 - 9.05: 6 Bond angle restraints: 29926 Sorted by residual: angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.29e+01 angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" CB LEU A 248 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C2 H35 A 701 " pdb=" N3 H35 A 701 " pdb=" C4 H35 A 701 " ideal model delta sigma weight residual 113.07 122.12 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C2 H35 B 701 " pdb=" N3 H35 B 701 " pdb=" C4 H35 B 701 " ideal model delta sigma weight residual 113.07 122.11 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" CAP H35 A 701 " pdb=" CAK H35 A 701 " pdb=" OAL H35 A 701 " ideal model delta sigma weight residual 118.02 126.33 -8.31 3.00e+00 1.11e-01 7.67e+00 ... (remaining 29921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7461 24.96 - 49.93: 296 49.93 - 74.89: 117 74.89 - 99.86: 4 99.86 - 124.82: 2 Dihedral angle restraints: 7880 sinusoidal: 4246 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 143.56 36.44 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CA PHE B 332 " pdb=" C PHE B 332 " pdb=" N ARG B 333 " pdb=" CA ARG B 333 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1324 0.099 - 0.199: 31 0.199 - 0.298: 0 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 270 " -0.094 2.00e-02 2.50e+03 7.85e-02 9.25e+01 pdb=" CG ASN B 270 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 270 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 270 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN B 270 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.033 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 122 1.98 - 2.63: 21588 2.63 - 3.29: 52563 3.29 - 3.94: 67232 3.94 - 4.60: 105585 Nonbonded interactions: 247090 Sorted by model distance: nonbonded pdb="HG23 THR A 162 " pdb=" HE1 PHE A 386 " model vdw 1.324 2.270 nonbonded pdb="HG21 THR A 162 " pdb=" HD2 PRO A 438 " model vdw 1.376 2.440 nonbonded pdb=" OD1 ASP A 130 " pdb=" HE2 HIS A 360 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP B 130 " pdb=" HE2 HIS B 360 " model vdw 1.603 2.450 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.606 2.450 ... (remaining 247085 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' } 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: 0.300 Extract box with map and model: 0.630 Check model and map are aligned: 0.190 Set scattering table: 0.180 Process input model: 38.920 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.004 0.102 8330 Z= 0.229 Angle : 0.612 9.054 11338 Z= 0.310 Chirality : 0.042 0.497 1356 Planarity : 0.004 0.058 1400 Dihedral : 13.359 124.823 2936 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.19 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 654 sheet: -5.81 (0.22), residues: 20 loop : -0.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 541 PHE 0.022 0.001 PHE A 203 TYR 0.010 0.001 TYR B 524 ARG 0.002 0.000 ARG A 454 *********************** 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 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.270 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 91 average time/residue: 2.3770 time to fit residues: 232.9799 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8486 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8330 Z= 0.273 Angle : 0.561 7.908 11338 Z= 0.297 Chirality : 0.041 0.135 1356 Planarity : 0.004 0.057 1400 Dihedral : 8.108 108.076 1238 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.70 % Allowed : 4.90 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.07 (0.26), residues: 1076 helix: 1.73 (0.20), residues: 648 sheet: -5.71 (0.30), residues: 20 loop : -0.59 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.013 0.002 PHE A 166 TYR 0.011 0.002 TYR B 27 ARG 0.002 0.000 ARG A 42 *********************** 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 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 1.339 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 2.4638 time to fit residues: 211.5489 Evaluate side-chains 78 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain A residue 126 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8330 Z= 0.190 Angle : 0.526 9.388 11338 Z= 0.274 Chirality : 0.040 0.155 1356 Planarity : 0.004 0.059 1400 Dihedral : 7.403 95.725 1234 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.70 % Allowed : 6.88 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.19 (0.26), residues: 1076 helix: 1.83 (0.20), residues: 648 sheet: -5.47 (0.42), residues: 20 loop : -0.56 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.015 0.001 PHE A 203 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG B 454 *********************** 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 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6939 (mpp) REVERT: A 494 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6965 (mpp) outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 2.4137 time to fit residues: 207.2123 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8457 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8330 Z= 0.175 Angle : 0.517 10.848 11338 Z= 0.267 Chirality : 0.039 0.129 1356 Planarity : 0.004 0.059 1400 Dihedral : 6.630 78.517 1234 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.93 % Allowed : 6.88 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.30 (0.26), residues: 1076 helix: 1.92 (0.20), residues: 654 sheet: -5.40 (0.44), residues: 20 loop : -0.56 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.019 0.001 PHE B 203 TYR 0.009 0.001 TYR A 388 ARG 0.001 0.000 ARG B 23 *********************** 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 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6922 (mpp) REVERT: B 520 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: A 494 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6923 (mpp) REVERT: A 509 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7260 (mt-10) REVERT: A 520 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8331 (mtt) outliers start: 8 outliers final: 0 residues processed: 83 average time/residue: 2.3798 time to fit residues: 212.2799 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 520 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8511 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8330 Z= 0.329 Angle : 0.582 10.863 11338 Z= 0.305 Chirality : 0.042 0.137 1356 Planarity : 0.005 0.059 1400 Dihedral : 5.908 49.410 1234 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.47 % Allowed : 9.44 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.99 (0.25), residues: 1076 helix: 1.69 (0.20), residues: 642 sheet: -5.21 (0.49), residues: 20 loop : -0.65 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 380 HIS 0.003 0.001 HIS B 350 PHE 0.018 0.002 PHE A 203 TYR 0.011 0.002 TYR B 388 ARG 0.003 0.001 ARG B 42 *********************** 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 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7007 (mpp) REVERT: A 494 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6995 (mpp) REVERT: A 509 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7304 (mt-10) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 2.5091 time to fit residues: 209.4717 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8509 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8330 Z= 0.301 Angle : 0.557 6.742 11338 Z= 0.294 Chirality : 0.041 0.146 1356 Planarity : 0.005 0.059 1400 Dihedral : 5.396 46.378 1234 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.93 % Allowed : 9.67 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.92 (0.25), residues: 1076 helix: 1.64 (0.20), residues: 642 sheet: -5.21 (0.50), residues: 20 loop : -0.71 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.003 0.001 HIS B 541 PHE 0.016 0.002 PHE B 203 TYR 0.011 0.002 TYR A 388 ARG 0.003 0.000 ARG A 23 *********************** 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 to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.292 Fit side-chains REVERT: B 494 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: A 494 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6987 (mpp) REVERT: A 509 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7318 (mt-10) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 2.5594 time to fit residues: 214.1038 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8330 Z= 0.152 Angle : 0.502 6.017 11338 Z= 0.264 Chirality : 0.039 0.140 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.095 45.864 1234 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.23 % Allowed : 10.49 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.22 (0.26), residues: 1076 helix: 1.89 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.014 0.001 PHE B 203 TYR 0.009 0.001 TYR A 388 ARG 0.004 0.000 ARG B 23 *********************** 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 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6960 (mpp) REVERT: A 494 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6942 (mpp) REVERT: A 509 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7316 (mt-10) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 2.5049 time to fit residues: 209.4728 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8330 Z= 0.260 Angle : 0.533 5.745 11338 Z= 0.281 Chirality : 0.040 0.150 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.165 44.656 1234 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 0.47 % Allowed : 10.49 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.11 (0.26), residues: 1076 helix: 1.82 (0.20), residues: 644 sheet: -5.17 (0.51), residues: 20 loop : -0.68 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 541 PHE 0.016 0.002 PHE B 203 TYR 0.009 0.001 TYR A 388 ARG 0.003 0.000 ARG A 23 *********************** 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 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6983 (mpp) REVERT: A 494 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6983 (mpp) REVERT: A 509 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7315 (mt-10) outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 2.5235 time to fit residues: 216.6676 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8330 Z= 0.169 Angle : 0.503 5.896 11338 Z= 0.264 Chirality : 0.039 0.142 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.033 44.422 1234 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.58 % Allowed : 10.26 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.25 (0.26), residues: 1076 helix: 1.93 (0.20), residues: 646 sheet: -5.20 (0.51), residues: 20 loop : -0.62 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.015 0.001 PHE B 203 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG B 23 *********************** 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 to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: A 494 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6966 (mpp) REVERT: A 509 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7304 (mt-10) outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 2.4522 time to fit residues: 210.8859 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8330 Z= 0.250 Angle : 0.533 5.717 11338 Z= 0.280 Chirality : 0.040 0.150 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.100 43.590 1234 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.58 % Allowed : 10.49 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.16 (0.26), residues: 1076 helix: 1.87 (0.20), residues: 644 sheet: -5.16 (0.50), residues: 20 loop : -0.69 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 541 PHE 0.015 0.002 PHE A 203 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG A 23 ********************** 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 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6982 (mpp) REVERT: A 494 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6986 (mpp) REVERT: A 509 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7313 (mt-10) outliers start: 5 outliers final: 2 residues processed: 81 average time/residue: 2.5401 time to fit residues: 222.7942 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.110959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.088864 restraints weight = 29332.853| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.66 r_work: 0.2829 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8330 Z= 0.227 Angle : 0.521 5.776 11338 Z= 0.274 Chirality : 0.040 0.148 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.086 43.385 1234 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.58 % Allowed : 10.49 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.18 (0.26), residues: 1076 helix: 1.89 (0.20), residues: 644 sheet: -5.18 (0.51), residues: 20 loop : -0.68 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.000 HIS B 541 PHE 0.015 0.001 PHE B 203 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5103.31 seconds wall clock time: 91 minutes 28.59 seconds (5488.59 seconds total)