Starting phenix.real_space_refine on Thu Feb 15 00:28:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7x_4746/02_2024/6r7x_4746_updated.pdb" } resolution = 3.47 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 54 5.16 5 C 7072 2.51 5 N 1644 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ASP 425": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10630 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5060 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 605} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5060 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 605} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 255 Unusual residues: {' CA': 3, 'PC1': 1, 'UMQ': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 60 Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 255 Unusual residues: {' CA': 3, 'PC1': 1, 'UMQ': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 60 Time building chain proxies: 6.09, per 1000 atoms: 0.57 Number of scatterers: 10630 At special positions: 0 Unit cell: (106.038, 104.394, 100.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 54 16.00 P 2 15.00 O 1852 8.00 N 1644 7.00 C 7072 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: 4.11 Conformation dependent library (CDL) restraints added in 1.8 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 60.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.280A pdb=" N THR A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 8.137A pdb=" N GLU A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N THR A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.426A pdb=" N ASP A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 272 removed outlier: 4.058A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 318 through 349 Processing helix chain 'A' and resid 361 through 385 removed outlier: 3.941A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 421 removed outlier: 5.522A pdb=" N SER A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 448 Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.998A pdb=" N GLN A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.952A pdb=" N LEU A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 removed outlier: 4.594A pdb=" N LEU A 524 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 530 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP A 533 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 576 removed outlier: 3.863A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 612 removed outlier: 4.045A pdb=" N ILE A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 640 removed outlier: 3.580A pdb=" N SER A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.281A pdb=" N THR B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 8.137A pdb=" N GLU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N THR B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 234 Proline residue: B 231 - end of helix Processing helix chain 'B' and resid 237 through 241 removed outlier: 4.426A pdb=" N ASP B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 272 removed outlier: 4.058A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 318 through 349 Processing helix chain 'B' and resid 361 through 385 removed outlier: 3.940A pdb=" N ARG B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 421 removed outlier: 5.523A pdb=" N SER B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 450 through 468 Processing helix chain 'B' and resid 476 through 486 removed outlier: 3.997A pdb=" N GLN B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.952A pdb=" N LEU B 501 " --> pdb=" O ASP B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 538 removed outlier: 4.594A pdb=" N LEU B 524 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 530 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP B 533 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.863A pdb=" N VAL B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 612 removed outlier: 4.045A pdb=" N ILE B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 640 removed outlier: 3.580A pdb=" N SER B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.537A pdb=" N GLN A 169 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 89 through 91 Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 Processing sheet with id= D, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.537A pdb=" N GLN B 169 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 Processing sheet with id= F, first strand: chain 'B' and resid 291 through 294 568 hydrogen bonds defined for protein. 1578 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: 2.96 Time building geometry restraints manager: 4.34 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: 1570 1.32 - 1.44: 3023 1.44 - 1.56: 6185 1.56 - 1.68: 4 1.68 - 1.81: 90 Bond restraints: 10872 Sorted by residual: bond pdb=" O13 PC1 B 905 " pdb=" P PC1 B 905 " ideal model delta sigma weight residual 1.652 1.594 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" O13 PC1 A 704 " pdb=" P PC1 A 704 " ideal model delta sigma weight residual 1.652 1.595 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O11 PC1 B 905 " pdb=" P PC1 B 905 " ideal model delta sigma weight residual 1.642 1.595 0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" O11 PC1 A 704 " pdb=" P PC1 A 704 " ideal model delta sigma weight residual 1.642 1.596 0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C11 PC1 B 905 " pdb=" O13 PC1 B 905 " ideal model delta sigma weight residual 1.407 1.451 -0.044 2.00e-02 2.50e+03 4.89e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 207 105.87 - 112.92: 5716 112.92 - 119.96: 4102 119.96 - 127.01: 4526 127.01 - 134.05: 117 Bond angle restraints: 14668 Sorted by residual: angle pdb=" C PHE A 204 " pdb=" N GLY A 205 " pdb=" CA GLY A 205 " ideal model delta sigma weight residual 121.45 115.10 6.35 1.54e+00 4.22e-01 1.70e+01 angle pdb=" C PHE B 204 " pdb=" N GLY B 205 " pdb=" CA GLY B 205 " ideal model delta sigma weight residual 121.45 115.12 6.33 1.54e+00 4.22e-01 1.69e+01 angle pdb=" N VAL B 357 " pdb=" CA VAL B 357 " pdb=" C VAL B 357 " ideal model delta sigma weight residual 112.50 107.05 5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 112.50 107.05 5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" C PHE B 235 " pdb=" N VAL B 236 " pdb=" CA VAL B 236 " ideal model delta sigma weight residual 121.97 128.93 -6.96 1.80e+00 3.09e-01 1.49e+01 ... (remaining 14663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 6422 24.56 - 49.11: 340 49.11 - 73.67: 36 73.67 - 98.22: 4 98.22 - 122.78: 8 Dihedral angle restraints: 6810 sinusoidal: 3080 harmonic: 3730 Sorted by residual: dihedral pdb=" CA ASN B 349 " pdb=" C ASN B 349 " pdb=" N SER B 350 " pdb=" CA SER B 350 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASN A 349 " pdb=" C ASN A 349 " pdb=" N SER A 350 " pdb=" CA SER A 350 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C5 UMQ B 906 " pdb=" C1 UMQ B 906 " pdb=" O5 UMQ B 906 " pdb=" O1 UMQ B 906 " ideal model delta sinusoidal sigma weight residual 298.22 175.44 122.78 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 6807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1210 0.042 - 0.083: 370 0.083 - 0.125: 67 0.125 - 0.167: 17 0.167 - 0.208: 12 Chirality restraints: 1676 Sorted by residual: chirality pdb=" C2 UMQ B 908 " pdb=" C1 UMQ B 908 " pdb=" C3 UMQ B 908 " pdb=" O2 UMQ B 908 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2 UMQ A 707 " pdb=" C1 UMQ A 707 " pdb=" C3 UMQ A 707 " pdb=" O2 UMQ A 707 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C2 UMQ A 705 " pdb=" C1 UMQ A 705 " pdb=" C3 UMQ A 705 " pdb=" O2 UMQ A 705 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1673 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 283 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 284 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 283 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 284 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 223 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 224 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " 0.030 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3028 2.81 - 3.33: 9119 3.33 - 3.86: 17181 3.86 - 4.38: 19436 4.38 - 4.90: 34483 Nonbonded interactions: 83247 Sorted by model distance: nonbonded pdb=" OE2 GLU A 500 " pdb="CA CA A 701 " model vdw 2.289 2.510 nonbonded pdb=" OE2 GLU B 500 " pdb="CA CA B 902 " model vdw 2.289 2.510 nonbonded pdb=" OH TYR A 211 " pdb=" OD2 ASP A 533 " model vdw 2.310 2.440 nonbonded pdb=" OH TYR B 211 " pdb=" OD2 ASP B 533 " model vdw 2.311 2.440 nonbonded pdb=" OE2 GLU A 448 " pdb="CA CA A 702 " model vdw 2.311 2.510 ... (remaining 83242 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' and (resid 13 through 641 or resid 702 through 703 or (resid 706 thro \ ugh 708 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF o \ r name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' or \ name O3' or name O5' or name O6')) or (resid 709 through 711 and (name CA or na \ me CB or name CG or name CD or name CH or name CC or name CF or name CI or name \ CJ or name CK or name CL )) or (resid 712 through 713 and (name CB or name CG or \ name CD or name CH or name CC or name CF or name CI or name CJ or name CK or na \ me CL )) or (resid 714 and (name CA or name CB or name CG or name CD or name CH \ or name CC or name CF or name CI or name CJ or name CK or name CL or name O1'))) \ ) selection = (chain 'B' and (resid 13 through 641 or resid 902 through 903 or (resid 906 thro \ ugh 908 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF o \ r name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' or \ name O3' or name O5' or name O6')) or (resid 909 through 911 and (name CA or na \ me CB or name CG or name CD or name CH or name CC or name CF or name CI or name \ CJ or name CK or name CL )) or (resid 912 through 913 and (name CB or name CG or \ name CD or name CH or name CC or name CF or name CI or name CJ or name CK or na \ me CL )) or resid 914)) } 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.120 Check model and map are aligned: 0.180 Set scattering table: 0.080 Process input model: 30.150 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.005 0.058 10872 Z= 0.328 Angle : 0.786 7.900 14668 Z= 0.422 Chirality : 0.045 0.208 1676 Planarity : 0.007 0.060 1750 Dihedral : 14.819 122.777 4402 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -3.00 (0.18), residues: 1254 helix: -1.92 (0.13), residues: 758 sheet: -0.83 (0.68), residues: 44 loop : -1.94 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 261 HIS 0.003 0.001 HIS B 347 PHE 0.016 0.002 PHE A 171 TYR 0.012 0.001 TYR A 377 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.171 Fit side-chains REVERT: A 36 LYS cc_start: 0.8317 (tttt) cc_final: 0.8080 (ttmm) REVERT: A 334 MET cc_start: 0.7935 (mmm) cc_final: 0.7694 (mmt) REVERT: A 339 MET cc_start: 0.7624 (ttm) cc_final: 0.7415 (ttm) REVERT: B 94 ASP cc_start: 0.8287 (p0) cc_final: 0.8075 (p0) REVERT: B 334 MET cc_start: 0.7951 (mmm) cc_final: 0.7693 (mmt) REVERT: B 339 MET cc_start: 0.7621 (ttm) cc_final: 0.7409 (ttm) REVERT: B 627 LEU cc_start: 0.8766 (tp) cc_final: 0.8352 (mp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2244 time to fit residues: 59.1923 Evaluate side-chains 128 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 504 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10872 Z= 0.188 Angle : 0.492 8.753 14668 Z= 0.245 Chirality : 0.036 0.155 1676 Planarity : 0.004 0.047 1750 Dihedral : 9.986 81.161 2038 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.67 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 7.45 % Favored : 91.23 % 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: -0.60 (0.22), residues: 1254 helix: 0.15 (0.17), residues: 782 sheet: -0.73 (0.70), residues: 44 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.003 0.001 HIS A 174 PHE 0.021 0.001 PHE A 584 TYR 0.007 0.001 TYR A 217 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.155 Fit side-chains REVERT: A 94 ASP cc_start: 0.8244 (p0) cc_final: 0.7956 (p0) REVERT: A 339 MET cc_start: 0.7613 (ttm) cc_final: 0.7318 (ttm) REVERT: B 94 ASP cc_start: 0.8213 (p0) cc_final: 0.8005 (p0) REVERT: B 339 MET cc_start: 0.7616 (ttm) cc_final: 0.7306 (ttm) outliers start: 14 outliers final: 7 residues processed: 142 average time/residue: 0.2210 time to fit residues: 45.1782 Evaluate side-chains 132 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10872 Z= 0.244 Angle : 0.502 6.604 14668 Z= 0.251 Chirality : 0.037 0.162 1676 Planarity : 0.004 0.045 1750 Dihedral : 9.299 59.720 2038 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.59 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 8.87 % Favored : 89.15 % 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: 0.48 (0.23), residues: 1254 helix: 1.05 (0.18), residues: 776 sheet: -0.67 (0.71), residues: 44 loop : -0.84 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 342 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.001 PHE A 584 TYR 0.018 0.001 TYR B 331 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.154 Fit side-chains REVERT: A 94 ASP cc_start: 0.8251 (p0) cc_final: 0.8016 (p0) REVERT: A 339 MET cc_start: 0.7641 (ttm) cc_final: 0.7321 (ttm) REVERT: B 94 ASP cc_start: 0.8225 (p0) cc_final: 0.7968 (p0) REVERT: B 339 MET cc_start: 0.7648 (ttm) cc_final: 0.7322 (ttm) outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 0.2225 time to fit residues: 46.1312 Evaluate side-chains 142 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10872 Z= 0.264 Angle : 0.500 6.633 14668 Z= 0.250 Chirality : 0.037 0.174 1676 Planarity : 0.003 0.043 1750 Dihedral : 8.961 57.195 2038 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 2.36 % Allowed : 9.72 % Favored : 87.92 % 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: 0.92 (0.24), residues: 1254 helix: 1.43 (0.19), residues: 770 sheet: -0.59 (0.71), residues: 44 loop : -0.67 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 342 HIS 0.004 0.001 HIS A 174 PHE 0.010 0.001 PHE A 337 TYR 0.007 0.001 TYR A 308 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.125 Fit side-chains REVERT: A 94 ASP cc_start: 0.8338 (p0) cc_final: 0.8121 (p0) REVERT: A 462 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8474 (mtm180) REVERT: B 339 MET cc_start: 0.7652 (ttm) cc_final: 0.7314 (ttm) outliers start: 25 outliers final: 20 residues processed: 139 average time/residue: 0.2427 time to fit residues: 49.2769 Evaluate side-chains 140 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 HIS ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10872 Z= 0.367 Angle : 0.556 7.805 14668 Z= 0.277 Chirality : 0.039 0.183 1676 Planarity : 0.004 0.044 1750 Dihedral : 9.367 59.866 2038 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.29 % Rotamer: Outliers : 2.92 % Allowed : 11.13 % Favored : 85.94 % 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: 0.91 (0.24), residues: 1254 helix: 1.38 (0.18), residues: 772 sheet: -0.75 (0.69), residues: 44 loop : -0.57 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE A 337 TYR 0.009 0.001 TYR A 327 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.182 Fit side-chains REVERT: A 462 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8470 (mtm180) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.2334 time to fit residues: 46.2010 Evaluate side-chains 140 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10872 Z= 0.182 Angle : 0.462 6.145 14668 Z= 0.232 Chirality : 0.036 0.196 1676 Planarity : 0.003 0.046 1750 Dihedral : 8.704 59.690 2038 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.59 % Favored : 98.25 % Rotamer: Outliers : 1.89 % Allowed : 13.11 % Favored : 85.00 % 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: 1.25 (0.24), residues: 1254 helix: 1.64 (0.18), residues: 786 sheet: -0.48 (0.73), residues: 44 loop : -0.51 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 261 HIS 0.003 0.001 HIS A 174 PHE 0.009 0.001 PHE A 584 TYR 0.007 0.001 TYR A 308 ARG 0.001 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.127 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 0.2111 time to fit residues: 41.6964 Evaluate side-chains 136 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10872 Z= 0.276 Angle : 0.508 6.866 14668 Z= 0.253 Chirality : 0.038 0.207 1676 Planarity : 0.004 0.044 1750 Dihedral : 8.731 58.231 2038 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.92 % Allowed : 13.21 % Favored : 83.87 % 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: 1.30 (0.24), residues: 1254 helix: 1.66 (0.18), residues: 784 sheet: -0.47 (0.74), residues: 44 loop : -0.43 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 342 HIS 0.004 0.001 HIS A 174 PHE 0.010 0.001 PHE A 337 TYR 0.019 0.001 TYR B 331 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.112 Fit side-chains outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.2235 time to fit residues: 44.1903 Evaluate side-chains 143 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 599 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10872 Z= 0.138 Angle : 0.446 7.487 14668 Z= 0.223 Chirality : 0.036 0.212 1676 Planarity : 0.003 0.046 1750 Dihedral : 7.975 56.975 2038 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.32 % Allowed : 14.81 % Favored : 83.87 % 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: 1.65 (0.24), residues: 1254 helix: 1.94 (0.18), residues: 788 sheet: -0.14 (0.77), residues: 44 loop : -0.34 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 261 HIS 0.002 0.001 HIS A 619 PHE 0.009 0.001 PHE A 584 TYR 0.007 0.001 TYR A 211 ARG 0.001 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.107 Fit side-chains REVERT: A 339 MET cc_start: 0.7589 (ttm) cc_final: 0.7270 (ttm) REVERT: B 175 ASP cc_start: 0.8327 (t0) cc_final: 0.8012 (t0) REVERT: B 339 MET cc_start: 0.7567 (ttm) cc_final: 0.7269 (ttm) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.2150 time to fit residues: 44.2092 Evaluate side-chains 130 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10872 Z= 0.120 Angle : 0.438 8.000 14668 Z= 0.219 Chirality : 0.035 0.218 1676 Planarity : 0.003 0.045 1750 Dihedral : 7.462 56.231 2038 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.47 % Allowed : 15.94 % Favored : 83.58 % 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: 1.90 (0.24), residues: 1254 helix: 2.10 (0.18), residues: 794 sheet: 0.86 (0.90), residues: 34 loop : -0.29 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 342 HIS 0.002 0.001 HIS A 390 PHE 0.009 0.001 PHE A 584 TYR 0.022 0.001 TYR B 331 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.173 Fit side-chains REVERT: A 175 ASP cc_start: 0.8287 (t0) cc_final: 0.8049 (t0) REVERT: A 339 MET cc_start: 0.7584 (ttm) cc_final: 0.7296 (ttm) REVERT: B 175 ASP cc_start: 0.8279 (t0) cc_final: 0.8031 (t0) REVERT: B 339 MET cc_start: 0.7612 (ttm) cc_final: 0.7284 (ttm) outliers start: 5 outliers final: 4 residues processed: 134 average time/residue: 0.2552 time to fit residues: 49.1508 Evaluate side-chains 132 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 0.0000 chunk 60 optimal weight: 0.0020 chunk 78 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 525 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10872 Z= 0.114 Angle : 0.433 8.348 14668 Z= 0.216 Chirality : 0.035 0.211 1676 Planarity : 0.003 0.045 1750 Dihedral : 7.086 56.934 2038 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.85 % Allowed : 15.47 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1254 helix: 2.20 (0.18), residues: 802 sheet: 1.26 (0.89), residues: 34 loop : -0.25 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 342 HIS 0.002 0.001 HIS A 390 PHE 0.013 0.001 PHE A 584 TYR 0.008 0.001 TYR A 211 ARG 0.002 0.000 ARG A 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.243 Fit side-chains REVERT: A 175 ASP cc_start: 0.8262 (t0) cc_final: 0.7992 (t0) REVERT: A 177 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 339 MET cc_start: 0.7601 (ttm) cc_final: 0.7285 (ttm) REVERT: B 175 ASP cc_start: 0.8237 (t0) cc_final: 0.7973 (t0) REVERT: B 339 MET cc_start: 0.7590 (ttm) cc_final: 0.7282 (ttm) outliers start: 9 outliers final: 6 residues processed: 141 average time/residue: 0.2241 time to fit residues: 45.4662 Evaluate side-chains 132 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096644 restraints weight = 12496.206| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.88 r_work: 0.2798 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10872 Z= 0.159 Angle : 0.461 8.497 14668 Z= 0.229 Chirality : 0.036 0.222 1676 Planarity : 0.003 0.045 1750 Dihedral : 7.219 56.557 2038 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.04 % Allowed : 15.75 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1254 helix: 2.18 (0.18), residues: 802 sheet: 0.47 (0.78), residues: 44 loop : -0.16 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 342 HIS 0.002 0.001 HIS A 174 PHE 0.012 0.001 PHE A 584 TYR 0.009 0.001 TYR B 102 ARG 0.002 0.000 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.92 seconds wall clock time: 41 minutes 53.51 seconds (2513.51 seconds total)