Starting phenix.real_space_refine on Fri Jul 19 15:07:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnx_41428/07_2024/8tnx_41428.cif" } resolution = 3.03 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5414 2.51 5 N 1352 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 250": "OD1" <-> "OD2" Residue "B ASP 250": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.63, per 1000 atoms: 0.68 Number of scatterers: 8272 At special positions: 0 Unit cell: (113.162, 96.642, 95.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1464 8.00 N 1352 7.00 C 5414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 94 through 102 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE A 475 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 526 through 547 removed outlier: 3.597A pdb=" N GLY A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 94 through 102 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL B 244 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 425 through 426 No H-bonds generated for 'chain 'B' and resid 425 through 426' Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE B 475 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 508 through 525 Processing helix chain 'B' and resid 526 through 547 removed outlier: 3.596A pdb=" N GLY B 534 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 711 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE A 580 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU A 556 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE A 578 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 583 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 683 " --> pdb=" O PHE A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE B 580 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 556 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE B 578 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 583 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE B 709 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 683 " --> pdb=" O PHE B 709 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1554 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: 2.41 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1287 1.32 - 1.44: 2271 1.44 - 1.57: 4824 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8442 Sorted by residual: bond pdb=" CA SER A 254 " pdb=" CB SER A 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 254 " pdb=" CB SER B 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 126 " pdb=" CB SER B 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.17e-02 7.31e+03 1.37e+01 ... (remaining 8437 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.17: 191 106.17 - 113.13: 4736 113.13 - 120.08: 2919 120.08 - 127.03: 3614 127.03 - 133.99: 78 Bond angle restraints: 11538 Sorted by residual: angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N ALA A 441 " pdb=" CA ALA A 441 " pdb=" C ALA A 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N THR A 443 " pdb=" CA THR A 443 " pdb=" C THR A 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N LEU A 440 " pdb=" CA LEU A 440 " pdb=" C LEU A 440 " ideal model delta sigma weight residual 113.40 102.81 10.59 1.47e+00 4.63e-01 5.19e+01 ... (remaining 11533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 4238 16.32 - 32.64: 460 32.64 - 48.96: 144 48.96 - 65.28: 36 65.28 - 81.61: 12 Dihedral angle restraints: 4890 sinusoidal: 1552 harmonic: 3338 Sorted by residual: dihedral pdb=" CD ARG A 58 " pdb=" NE ARG A 58 " pdb=" CZ ARG A 58 " pdb=" NH1 ARG A 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CD ARG B 58 " pdb=" NE ARG B 58 " pdb=" CZ ARG B 58 " pdb=" NH1 ARG B 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" N LEU A 468 " pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sinusoidal sigma weight residual -60.00 -119.18 59.18 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 965 0.044 - 0.088: 269 0.088 - 0.132: 139 0.132 - 0.176: 48 0.176 - 0.220: 21 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA LEU B 491 " pdb=" N LEU B 491 " pdb=" C LEU B 491 " pdb=" CB LEU B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 491 " pdb=" N LEU A 491 " pdb=" C LEU A 491 " pdb=" CB LEU A 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 444 " pdb=" N LEU A 444 " pdb=" C LEU A 444 " pdb=" CB LEU A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1439 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 58 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG B 58 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 58 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 58 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 58 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 58 " 1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG A 58 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 58 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 58 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 58 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 159 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C HIS B 159 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS B 159 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 160 " -0.019 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2277 2.80 - 3.33: 8170 3.33 - 3.85: 13985 3.85 - 4.38: 15915 4.38 - 4.90: 27421 Nonbonded interactions: 67768 Sorted by model distance: nonbonded pdb=" O MET B 220 " pdb=" OG1 THR B 224 " model vdw 2.278 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 224 " model vdw 2.278 2.440 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 126 " model vdw 2.296 2.440 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 126 " model vdw 2.296 2.440 nonbonded pdb=" O SER B 126 " pdb=" OG SER B 130 " model vdw 2.329 2.440 ... (remaining 67763 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' } 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 0.095 8442 Z= 0.437 Angle : 0.901 11.203 11538 Z= 0.645 Chirality : 0.058 0.220 1442 Planarity : 0.018 0.467 1420 Dihedral : 16.340 81.606 2734 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.83 % Favored : 96.82 % Rotamer: Outliers : 4.12 % Allowed : 25.62 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1132 helix: 0.35 (0.19), residues: 754 sheet: 1.76 (0.72), residues: 50 loop : -0.73 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 376 HIS 0.003 0.001 HIS B 363 PHE 0.013 0.001 PHE B 434 TYR 0.015 0.001 TYR B 588 ARG 0.001 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 0.865 Fit side-chains REVERT: A 238 PHE cc_start: 0.7371 (t80) cc_final: 0.7106 (t80) REVERT: A 239 PHE cc_start: 0.6150 (m-80) cc_final: 0.5929 (m-10) REVERT: A 270 LYS cc_start: 0.7068 (mtmt) cc_final: 0.6532 (ttpp) REVERT: A 489 VAL cc_start: 0.8078 (t) cc_final: 0.7871 (t) REVERT: A 490 ASN cc_start: 0.7544 (m110) cc_final: 0.7318 (m-40) REVERT: A 716 MET cc_start: 0.7895 (mmm) cc_final: 0.7635 (mmm) REVERT: B 238 PHE cc_start: 0.7370 (t80) cc_final: 0.7107 (t80) REVERT: B 239 PHE cc_start: 0.6147 (m-80) cc_final: 0.5930 (m-10) REVERT: B 270 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6530 (ttpp) REVERT: B 489 VAL cc_start: 0.8076 (t) cc_final: 0.7868 (t) REVERT: B 490 ASN cc_start: 0.7539 (m110) cc_final: 0.7315 (m-40) REVERT: B 716 MET cc_start: 0.7896 (mmm) cc_final: 0.7633 (mmm) outliers start: 33 outliers final: 13 residues processed: 176 average time/residue: 0.1769 time to fit residues: 44.2441 Evaluate side-chains 124 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.0170 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 432 HIS A 490 ASN A 685 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 432 HIS B 490 ASN B 547 GLN B 685 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8442 Z= 0.187 Angle : 0.540 7.441 11538 Z= 0.279 Chirality : 0.040 0.130 1442 Planarity : 0.004 0.043 1420 Dihedral : 5.866 54.191 1225 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.50 % Allowed : 21.25 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1132 helix: 1.19 (0.19), residues: 768 sheet: 1.64 (0.73), residues: 50 loop : -0.15 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.002 0.001 HIS A 665 PHE 0.013 0.001 PHE A 434 TYR 0.019 0.001 TYR A 151 ARG 0.004 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 0.902 Fit side-chains REVERT: A 239 PHE cc_start: 0.6285 (m-80) cc_final: 0.5905 (m-10) REVERT: A 270 LYS cc_start: 0.6854 (mtmt) cc_final: 0.6167 (tttp) REVERT: A 490 ASN cc_start: 0.7571 (m-40) cc_final: 0.7344 (m-40) REVERT: B 239 PHE cc_start: 0.6285 (m-80) cc_final: 0.5905 (m-10) REVERT: B 270 LYS cc_start: 0.6852 (mtmt) cc_final: 0.6167 (tttp) REVERT: B 490 ASN cc_start: 0.7575 (m-40) cc_final: 0.7346 (m-40) outliers start: 36 outliers final: 24 residues processed: 148 average time/residue: 0.1937 time to fit residues: 39.8972 Evaluate side-chains 134 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 721 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.0070 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8442 Z= 0.186 Angle : 0.507 7.019 11538 Z= 0.259 Chirality : 0.040 0.155 1442 Planarity : 0.003 0.037 1420 Dihedral : 5.652 57.968 1220 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.50 % Allowed : 22.88 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1132 helix: 1.43 (0.19), residues: 762 sheet: 1.37 (0.70), residues: 50 loop : -0.07 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 290 HIS 0.002 0.000 HIS A 647 PHE 0.015 0.001 PHE A 145 TYR 0.015 0.001 TYR B 151 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.948 Fit side-chains REVERT: A 270 LYS cc_start: 0.6785 (mtmt) cc_final: 0.6310 (ttpp) REVERT: A 418 MET cc_start: 0.6785 (tpp) cc_final: 0.6551 (tpp) REVERT: A 672 ARG cc_start: 0.7525 (ttp80) cc_final: 0.6862 (ttp80) REVERT: B 270 LYS cc_start: 0.6781 (mtmt) cc_final: 0.6306 (ttpp) REVERT: B 418 MET cc_start: 0.6788 (tpp) cc_final: 0.6554 (tpp) REVERT: B 672 ARG cc_start: 0.7498 (ttp80) cc_final: 0.6844 (ttp80) outliers start: 28 outliers final: 19 residues processed: 150 average time/residue: 0.1804 time to fit residues: 38.5372 Evaluate side-chains 144 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.0170 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8442 Z= 0.175 Angle : 0.490 6.307 11538 Z= 0.249 Chirality : 0.039 0.128 1442 Planarity : 0.003 0.033 1420 Dihedral : 5.195 47.535 1218 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.25 % Allowed : 23.25 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1132 helix: 1.55 (0.19), residues: 768 sheet: 1.39 (0.70), residues: 50 loop : -0.04 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.001 0.000 HIS A 298 PHE 0.014 0.001 PHE A 434 TYR 0.016 0.001 TYR A 151 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.161 Fit side-chains REVERT: A 270 LYS cc_start: 0.6697 (mtmt) cc_final: 0.6316 (ttpp) REVERT: A 418 MET cc_start: 0.6820 (tpp) cc_final: 0.6542 (tpp) REVERT: A 672 ARG cc_start: 0.7508 (ttp80) cc_final: 0.6864 (ttp80) REVERT: B 270 LYS cc_start: 0.6696 (mtmt) cc_final: 0.6314 (ttpp) REVERT: B 418 MET cc_start: 0.6824 (tpp) cc_final: 0.6545 (tpp) REVERT: B 672 ARG cc_start: 0.7516 (ttp80) cc_final: 0.6871 (ttp80) outliers start: 26 outliers final: 23 residues processed: 148 average time/residue: 0.1856 time to fit residues: 38.5549 Evaluate side-chains 147 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8442 Z= 0.384 Angle : 0.623 9.417 11538 Z= 0.315 Chirality : 0.044 0.143 1442 Planarity : 0.004 0.033 1420 Dihedral : 5.416 48.832 1216 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.12 % Allowed : 22.12 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1132 helix: 1.25 (0.19), residues: 768 sheet: 1.28 (0.76), residues: 50 loop : -0.35 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 505 HIS 0.003 0.001 HIS A 647 PHE 0.019 0.002 PHE B 658 TYR 0.016 0.002 TYR B 232 ARG 0.003 0.001 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 0.968 Fit side-chains REVERT: A 270 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6473 (ttpp) REVERT: B 270 LYS cc_start: 0.7042 (mtmt) cc_final: 0.6473 (ttpp) outliers start: 33 outliers final: 25 residues processed: 157 average time/residue: 0.1778 time to fit residues: 39.4597 Evaluate side-chains 153 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 721 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8442 Z= 0.176 Angle : 0.520 8.068 11538 Z= 0.259 Chirality : 0.039 0.126 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.217 49.728 1216 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.88 % Allowed : 23.38 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1132 helix: 1.50 (0.19), residues: 768 sheet: 1.29 (0.75), residues: 50 loop : -0.19 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS A 647 PHE 0.014 0.001 PHE B 434 TYR 0.014 0.001 TYR B 151 ARG 0.003 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.887 Fit side-chains REVERT: A 270 LYS cc_start: 0.7007 (mtmt) cc_final: 0.6366 (ttpp) REVERT: A 672 ARG cc_start: 0.7465 (ttp80) cc_final: 0.6870 (ttm170) REVERT: B 270 LYS cc_start: 0.7010 (mtmt) cc_final: 0.6367 (ttpp) REVERT: B 672 ARG cc_start: 0.7458 (ttp80) cc_final: 0.6864 (ttm170) outliers start: 23 outliers final: 21 residues processed: 149 average time/residue: 0.1813 time to fit residues: 37.8904 Evaluate side-chains 152 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8442 Z= 0.237 Angle : 0.537 8.702 11538 Z= 0.267 Chirality : 0.040 0.132 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.153 50.086 1216 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.88 % Allowed : 23.00 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1132 helix: 1.51 (0.19), residues: 768 sheet: 1.31 (0.76), residues: 50 loop : -0.25 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.001 0.000 HIS A 647 PHE 0.016 0.002 PHE B 434 TYR 0.014 0.001 TYR B 151 ARG 0.004 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.951 Fit side-chains REVERT: A 136 GLU cc_start: 0.7222 (mp0) cc_final: 0.6579 (mt-10) REVERT: A 270 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6420 (ttpp) REVERT: A 672 ARG cc_start: 0.7496 (ttp80) cc_final: 0.6876 (ttp80) REVERT: B 136 GLU cc_start: 0.7227 (mp0) cc_final: 0.6584 (mt-10) REVERT: B 270 LYS cc_start: 0.6971 (mtmt) cc_final: 0.6422 (ttpp) REVERT: B 672 ARG cc_start: 0.7487 (ttp80) cc_final: 0.6876 (ttp80) outliers start: 23 outliers final: 21 residues processed: 149 average time/residue: 0.2032 time to fit residues: 42.4332 Evaluate side-chains 153 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.0170 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8442 Z= 0.158 Angle : 0.496 8.098 11538 Z= 0.246 Chirality : 0.039 0.125 1442 Planarity : 0.003 0.031 1420 Dihedral : 4.997 49.700 1216 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.88 % Allowed : 23.75 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1132 helix: 1.69 (0.19), residues: 768 sheet: 1.42 (0.75), residues: 50 loop : -0.08 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.001 0.000 HIS A 298 PHE 0.013 0.001 PHE B 434 TYR 0.014 0.001 TYR B 151 ARG 0.003 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.903 Fit side-chains REVERT: A 136 GLU cc_start: 0.7058 (mp0) cc_final: 0.6433 (mt-10) REVERT: A 270 LYS cc_start: 0.6965 (mtmt) cc_final: 0.6364 (ttpp) REVERT: A 672 ARG cc_start: 0.7490 (ttp80) cc_final: 0.6877 (ttp80) REVERT: B 136 GLU cc_start: 0.7065 (mp0) cc_final: 0.6440 (mt-10) REVERT: B 270 LYS cc_start: 0.6965 (mtmt) cc_final: 0.6363 (ttpp) REVERT: B 672 ARG cc_start: 0.7524 (ttp80) cc_final: 0.6892 (ttp80) outliers start: 23 outliers final: 21 residues processed: 145 average time/residue: 0.2282 time to fit residues: 46.2069 Evaluate side-chains 149 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8442 Z= 0.180 Angle : 0.504 8.390 11538 Z= 0.249 Chirality : 0.039 0.123 1442 Planarity : 0.003 0.031 1420 Dihedral : 4.951 49.174 1216 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.88 % Allowed : 23.88 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1132 helix: 1.82 (0.19), residues: 762 sheet: 1.50 (0.76), residues: 50 loop : -0.23 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.001 0.000 HIS B 292 PHE 0.014 0.001 PHE B 434 TYR 0.013 0.001 TYR A 151 ARG 0.003 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.935 Fit side-chains REVERT: A 136 GLU cc_start: 0.7051 (mp0) cc_final: 0.6457 (mt-10) REVERT: A 270 LYS cc_start: 0.6926 (mtmt) cc_final: 0.6380 (ttpp) REVERT: A 672 ARG cc_start: 0.7503 (ttp80) cc_final: 0.6888 (ttp80) REVERT: B 136 GLU cc_start: 0.7059 (mp0) cc_final: 0.6465 (mt-10) REVERT: B 270 LYS cc_start: 0.6927 (mtmt) cc_final: 0.6381 (ttpp) REVERT: B 672 ARG cc_start: 0.7537 (ttp80) cc_final: 0.6907 (ttp80) outliers start: 23 outliers final: 21 residues processed: 145 average time/residue: 0.1913 time to fit residues: 38.9221 Evaluate side-chains 147 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8442 Z= 0.195 Angle : 0.515 8.307 11538 Z= 0.253 Chirality : 0.039 0.126 1442 Planarity : 0.003 0.032 1420 Dihedral : 4.937 48.343 1216 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.62 % Allowed : 24.12 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1132 helix: 1.76 (0.19), residues: 768 sheet: 1.49 (0.76), residues: 50 loop : -0.15 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.001 0.000 HIS B 292 PHE 0.014 0.001 PHE A 434 TYR 0.013 0.001 TYR B 151 ARG 0.003 0.000 ARG B 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.954 Fit side-chains REVERT: A 136 GLU cc_start: 0.7086 (mp0) cc_final: 0.6531 (mt-10) REVERT: A 270 LYS cc_start: 0.6932 (mtmt) cc_final: 0.6441 (ttpp) REVERT: A 672 ARG cc_start: 0.7537 (ttp80) cc_final: 0.6885 (ttp80) REVERT: B 136 GLU cc_start: 0.7095 (mp0) cc_final: 0.6540 (mt-10) REVERT: B 270 LYS cc_start: 0.6933 (mtmt) cc_final: 0.6441 (ttpp) REVERT: B 672 ARG cc_start: 0.7534 (ttp80) cc_final: 0.6887 (ttp80) outliers start: 21 outliers final: 21 residues processed: 145 average time/residue: 0.1866 time to fit residues: 37.9147 Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.193617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137105 restraints weight = 8226.023| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.57 r_work: 0.3447 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8442 Z= 0.184 Angle : 0.514 8.301 11538 Z= 0.251 Chirality : 0.039 0.124 1442 Planarity : 0.003 0.032 1420 Dihedral : 4.940 48.223 1216 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.62 % Allowed : 23.88 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1132 helix: 1.85 (0.19), residues: 762 sheet: 1.52 (0.76), residues: 50 loop : -0.29 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 98 HIS 0.001 0.000 HIS B 432 PHE 0.014 0.001 PHE A 434 TYR 0.013 0.001 TYR A 151 ARG 0.003 0.000 ARG B 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.31 seconds wall clock time: 36 minutes 57.12 seconds (2217.12 seconds total)