Starting phenix.real_space_refine on Tue Feb 13 16:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7u_33048/02_2024/7x7u_33048.pdb" } resolution = 3.77 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= 0.012 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 26 5.16 5 C 4348 2.51 5 N 1135 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.25, per 1000 atoms: 0.62 Number of scatterers: 6862 At special positions: 0 Unit cell: (107.364, 113.588, 85.58, 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 26 16.00 O 1353 8.00 N 1135 7.00 C 4348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.02 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 4.4% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'G' and resid 365 through 370 removed outlier: 4.010A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 365 through 370' Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.920A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 3.687A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.567A pdb=" N GLU H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.651A pdb=" N GLY A 105 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.136A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.625A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.553A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE L 79 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP L 74 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 71 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.716A pdb=" N LEU L 11 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR L 106 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.783A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.516A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.358A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.664A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.595A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.574A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 102 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 86 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.866A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.686A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 81 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR A 116 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR A 116 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.006A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 67 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.601A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.591A pdb=" N VAL C 20 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 81 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.937A pdb=" N ILE C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 94 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.663A pdb=" N LYS C 98 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 111 " --> pdb=" O LYS C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 153 hydrogen bonds defined for protein. 363 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: 1.77 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1124 1.31 - 1.44: 2122 1.44 - 1.56: 3760 1.56 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 7037 Sorted by residual: bond pdb=" N ALA G 397 " pdb=" CA ALA G 397 " ideal model delta sigma weight residual 1.461 1.404 0.057 1.38e-02 5.25e+03 1.73e+01 bond pdb=" CA ALA G 397 " pdb=" CB ALA G 397 " ideal model delta sigma weight residual 1.526 1.468 0.059 1.53e-02 4.27e+03 1.47e+01 bond pdb=" C GLN G 493 " pdb=" O GLN G 493 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.18e-02 7.18e+03 1.44e+01 bond pdb=" C GLU L 97 " pdb=" O GLU L 97 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.46e-02 4.69e+03 1.30e+01 bond pdb=" CA GLN G 493 " pdb=" C GLN G 493 " ideal model delta sigma weight residual 1.520 1.478 0.042 1.22e-02 6.72e+03 1.19e+01 ... (remaining 7032 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.51: 124 105.51 - 112.65: 3526 112.65 - 119.79: 2283 119.79 - 126.93: 3534 126.93 - 134.07: 95 Bond angle restraints: 9562 Sorted by residual: angle pdb=" N GLY G 416 " pdb=" CA GLY G 416 " pdb=" C GLY G 416 " ideal model delta sigma weight residual 111.85 103.25 8.60 1.06e+00 8.90e-01 6.59e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" N LYS G 417 " ideal model delta sigma weight residual 114.23 118.84 -4.61 8.80e-01 1.29e+00 2.75e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 121.48 131.03 -9.55 2.04e+00 2.40e-01 2.19e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" O GLY G 416 " ideal model delta sigma weight residual 122.33 118.55 3.78 8.10e-01 1.52e+00 2.17e+01 angle pdb=" CA GLU L 97 " pdb=" C GLU L 97 " pdb=" N ILE L 98 " ideal model delta sigma weight residual 116.34 121.09 -4.75 1.04e+00 9.25e-01 2.09e+01 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3588 15.05 - 30.10: 397 30.10 - 45.14: 98 45.14 - 60.19: 14 60.19 - 75.24: 7 Dihedral angle restraints: 4104 sinusoidal: 1580 harmonic: 2524 Sorted by residual: dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 138.75 41.25 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA PRO G 337 " pdb=" C PRO G 337 " pdb=" N PHE G 338 " pdb=" CA PHE G 338 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE G 472 " pdb=" C ILE G 472 " pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 834 0.067 - 0.135: 151 0.135 - 0.202: 30 0.202 - 0.269: 4 0.269 - 0.336: 3 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE L 98 " pdb=" CA ILE L 98 " pdb=" CG1 ILE L 98 " pdb=" CG2 ILE L 98 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLU G 406 " pdb=" N GLU G 406 " pdb=" C GLU G 406 " pdb=" CB GLU G 406 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL G 407 " pdb=" N VAL G 407 " pdb=" C VAL G 407 " pdb=" CB VAL G 407 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1019 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 62 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO L 63 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 521 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 59 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.033 5.00e-02 4.00e+02 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1936 2.80 - 3.33: 5210 3.33 - 3.85: 10906 3.85 - 4.38: 11873 4.38 - 4.90: 22003 Nonbonded interactions: 51928 Sorted by model distance: nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.276 2.440 nonbonded pdb=" OD1 ASP G 442 " pdb=" OH TYR G 451 " model vdw 2.309 2.440 nonbonded pdb=" OG SER D 49 " pdb=" OE2 GLU D 55 " model vdw 2.314 2.440 nonbonded pdb=" O SER B 60 " pdb=" OG SER B 60 " model vdw 2.318 2.440 nonbonded pdb=" O GLN B 3 " pdb=" OG SER B 26 " model vdw 2.330 2.440 ... (remaining 51923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.270 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: 0.000 Extract box with map and model: 38.970 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 0.071 7037 Z= 0.446 Angle : 0.938 11.497 9562 Z= 0.556 Chirality : 0.058 0.336 1022 Planarity : 0.007 0.070 1228 Dihedral : 13.548 75.239 2490 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.10 (0.24), residues: 864 helix: -3.58 (0.91), residues: 21 sheet: -2.52 (0.26), residues: 338 loop : -2.90 (0.22), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 436 HIS 0.006 0.001 HIS B 55 PHE 0.031 0.002 PHE G 377 TYR 0.025 0.002 TYR B 49 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8236 (mp10) cc_final: 0.7610 (mp10) REVERT: G 456 PHE cc_start: 0.7244 (t80) cc_final: 0.6684 (t80) REVERT: G 518 LEU cc_start: 0.7200 (tt) cc_final: 0.6931 (tp) REVERT: G 525 CYS cc_start: 0.7450 (m) cc_final: 0.7232 (m) REVERT: L 27 GLN cc_start: 0.7391 (mt0) cc_final: 0.7018 (mt0) REVERT: L 56 SER cc_start: 0.8802 (t) cc_final: 0.8323 (m) REVERT: L 83 GLU cc_start: 0.7568 (mp0) cc_final: 0.7195 (mp0) REVERT: H 18 VAL cc_start: 0.8191 (t) cc_final: 0.7937 (p) REVERT: H 82 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7383 (mt-10) REVERT: H 113 GLN cc_start: 0.7425 (mp10) cc_final: 0.7128 (mp10) REVERT: B 4 MET cc_start: 0.7534 (mmm) cc_final: 0.6956 (mmt) REVERT: B 37 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 19 LYS cc_start: 0.7910 (tttt) cc_final: 0.7507 (tttp) REVERT: A 25 SER cc_start: 0.8729 (p) cc_final: 0.8499 (m) REVERT: A 34 MET cc_start: 0.8094 (tpp) cc_final: 0.7772 (tpp) REVERT: A 64 PHE cc_start: 0.8346 (m-80) cc_final: 0.8067 (m-80) REVERT: A 65 LYS cc_start: 0.7229 (tttp) cc_final: 0.6979 (tptp) REVERT: A 82 GLN cc_start: 0.7008 (tt0) cc_final: 0.6479 (tm-30) REVERT: A 111 GLN cc_start: 0.7920 (tp40) cc_final: 0.7229 (pm20) REVERT: D 27 ASP cc_start: 0.8991 (t0) cc_final: 0.8538 (t0) REVERT: C 2 ILE cc_start: 0.7861 (mm) cc_final: 0.7316 (mm) REVERT: C 4 LEU cc_start: 0.7411 (mt) cc_final: 0.7193 (mt) REVERT: C 10 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 23 LYS cc_start: 0.8262 (tttt) cc_final: 0.8025 (tttp) REVERT: C 41 HIS cc_start: 0.7657 (t70) cc_final: 0.7251 (t-170) REVERT: C 43 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7857 (mptt) REVERT: C 84 ASN cc_start: 0.8439 (p0) cc_final: 0.7947 (p0) REVERT: C 85 SER cc_start: 0.8982 (m) cc_final: 0.8441 (p) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.1983 time to fit residues: 57.4984 Evaluate side-chains 173 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 450 ASN L 57 ASN H 5 GLN B 27 GLN B 55 HIS D 28 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7037 Z= 0.261 Angle : 0.599 7.608 9562 Z= 0.319 Chirality : 0.043 0.156 1022 Planarity : 0.004 0.047 1228 Dihedral : 5.714 34.727 989 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.06 % Allowed : 15.02 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.48 (0.26), residues: 864 helix: -4.64 (0.48), residues: 21 sheet: -2.10 (0.27), residues: 347 loop : -2.39 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 PHE 0.017 0.001 PHE G 377 TYR 0.026 0.001 TYR B 49 ARG 0.006 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.771 Fit side-chains REVERT: G 414 GLN cc_start: 0.8183 (mp10) cc_final: 0.7413 (mp10) REVERT: G 456 PHE cc_start: 0.7301 (t80) cc_final: 0.6687 (t80) REVERT: G 465 GLU cc_start: 0.7587 (tt0) cc_final: 0.7126 (tp30) REVERT: L 27 GLN cc_start: 0.7544 (mt0) cc_final: 0.7141 (mt0) REVERT: L 56 SER cc_start: 0.8529 (t) cc_final: 0.8006 (m) REVERT: L 83 GLU cc_start: 0.7645 (mp0) cc_final: 0.7339 (mp0) REVERT: H 18 VAL cc_start: 0.7448 (t) cc_final: 0.7025 (p) REVERT: H 82 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7059 (mt-10) REVERT: H 113 GLN cc_start: 0.7260 (mp10) cc_final: 0.6774 (mp10) REVERT: B 4 MET cc_start: 0.7176 (mmm) cc_final: 0.6842 (mmt) REVERT: B 37 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 61 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.6454 (mtm-85) REVERT: A 19 LYS cc_start: 0.7901 (tttt) cc_final: 0.7482 (tttp) REVERT: A 32 TYR cc_start: 0.9016 (m-10) cc_final: 0.8709 (m-80) REVERT: A 40 ARG cc_start: 0.7232 (mmm-85) cc_final: 0.6897 (mmm-85) REVERT: A 74 LYS cc_start: 0.7024 (mtpt) cc_final: 0.6817 (mtmm) REVERT: A 111 GLN cc_start: 0.7888 (tp40) cc_final: 0.7246 (pm20) REVERT: D 27 ASP cc_start: 0.8976 (t0) cc_final: 0.8712 (t70) REVERT: C 2 ILE cc_start: 0.7610 (mm) cc_final: 0.7243 (mm) REVERT: C 10 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 19 LYS cc_start: 0.7976 (pttt) cc_final: 0.7708 (pptt) REVERT: C 41 HIS cc_start: 0.7688 (t70) cc_final: 0.7198 (t-90) REVERT: C 43 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7831 (mptt) REVERT: C 54 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8199 (p90) REVERT: C 84 ASN cc_start: 0.8543 (p0) cc_final: 0.8320 (p0) REVERT: C 85 SER cc_start: 0.9067 (m) cc_final: 0.8690 (p) REVERT: C 98 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6592 (pttp) outliers start: 30 outliers final: 17 residues processed: 199 average time/residue: 0.1948 time to fit residues: 50.7497 Evaluate side-chains 182 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 55 HIS D 90 GLN C 82 HIS C 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7037 Z= 0.156 Angle : 0.526 7.141 9562 Z= 0.278 Chirality : 0.041 0.140 1022 Planarity : 0.004 0.041 1228 Dihedral : 4.866 30.057 989 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.57 % Allowed : 18.54 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.99 (0.27), residues: 864 helix: -4.71 (0.45), residues: 21 sheet: -1.66 (0.27), residues: 343 loop : -2.12 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 PHE 0.011 0.001 PHE G 377 TYR 0.021 0.001 TYR A 27 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.778 Fit side-chains REVERT: G 414 GLN cc_start: 0.8048 (mp10) cc_final: 0.7484 (mp10) REVERT: G 440 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8314 (p0) REVERT: G 456 PHE cc_start: 0.7226 (t80) cc_final: 0.6661 (t80) REVERT: L 27 GLN cc_start: 0.7612 (mt0) cc_final: 0.7219 (mt0) REVERT: L 83 GLU cc_start: 0.7698 (mp0) cc_final: 0.7421 (mp0) REVERT: H 18 VAL cc_start: 0.7194 (t) cc_final: 0.6907 (p) REVERT: H 113 GLN cc_start: 0.7361 (mp10) cc_final: 0.6964 (mp10) REVERT: B 4 MET cc_start: 0.7065 (mmm) cc_final: 0.6777 (mmt) REVERT: B 30 SER cc_start: 0.8471 (t) cc_final: 0.8205 (p) REVERT: B 37 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7243 (tm-30) REVERT: B 61 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6556 (mtm-85) REVERT: A 19 LYS cc_start: 0.7812 (tttt) cc_final: 0.7427 (tttp) REVERT: A 32 TYR cc_start: 0.8932 (m-80) cc_final: 0.8577 (m-80) REVERT: A 34 MET cc_start: 0.8361 (ttm) cc_final: 0.7977 (ttm) REVERT: A 111 GLN cc_start: 0.7890 (tp40) cc_final: 0.7249 (pm20) REVERT: D 27 ASP cc_start: 0.9039 (t0) cc_final: 0.8603 (t70) REVERT: C 10 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 19 LYS cc_start: 0.7926 (pttt) cc_final: 0.7694 (pptt) REVERT: C 41 HIS cc_start: 0.7656 (t70) cc_final: 0.7171 (t-90) REVERT: C 43 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7817 (mptt) REVERT: C 54 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 84 ASN cc_start: 0.8580 (p0) cc_final: 0.8367 (p0) REVERT: C 85 SER cc_start: 0.9048 (m) cc_final: 0.8739 (p) REVERT: C 99 GLU cc_start: 0.7208 (pt0) cc_final: 0.6909 (pt0) outliers start: 19 outliers final: 10 residues processed: 190 average time/residue: 0.1879 time to fit residues: 47.4155 Evaluate side-chains 182 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN B 55 HIS D 38 GLN C 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7037 Z= 0.201 Angle : 0.526 7.076 9562 Z= 0.278 Chirality : 0.041 0.146 1022 Planarity : 0.003 0.037 1228 Dihedral : 4.739 30.161 989 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.74 % Allowed : 18.27 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.76 (0.27), residues: 864 helix: -4.74 (0.45), residues: 21 sheet: -1.54 (0.26), residues: 359 loop : -1.92 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 PHE 0.015 0.001 PHE G 377 TYR 0.020 0.001 TYR A 27 ARG 0.005 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 0.992 Fit side-chains REVERT: G 414 GLN cc_start: 0.8058 (mp10) cc_final: 0.7457 (mp10) REVERT: G 440 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8353 (p0) REVERT: G 456 PHE cc_start: 0.7241 (t80) cc_final: 0.6659 (t80) REVERT: G 465 GLU cc_start: 0.7462 (tt0) cc_final: 0.7100 (tp30) REVERT: L 27 GLN cc_start: 0.7567 (mt0) cc_final: 0.7148 (mt0) REVERT: L 83 GLU cc_start: 0.7683 (mp0) cc_final: 0.7416 (mp0) REVERT: H 18 VAL cc_start: 0.7338 (t) cc_final: 0.7011 (p) REVERT: B 30 SER cc_start: 0.8560 (t) cc_final: 0.8336 (p) REVERT: B 37 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 19 LYS cc_start: 0.7856 (tttt) cc_final: 0.7498 (tttp) REVERT: A 32 TYR cc_start: 0.8968 (m-80) cc_final: 0.8675 (m-80) REVERT: A 34 MET cc_start: 0.8393 (ttm) cc_final: 0.8000 (ttm) REVERT: A 111 GLN cc_start: 0.7948 (tp40) cc_final: 0.7270 (pm20) REVERT: D 4 MET cc_start: 0.8568 (mmm) cc_final: 0.8202 (mmm) REVERT: D 27 ASP cc_start: 0.9030 (t0) cc_final: 0.8576 (t70) REVERT: C 10 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 19 LYS cc_start: 0.7932 (pttt) cc_final: 0.7686 (pptt) REVERT: C 41 HIS cc_start: 0.7643 (t70) cc_final: 0.7154 (t-90) REVERT: C 43 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7822 (mptt) REVERT: C 54 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7903 (p90) REVERT: C 84 ASN cc_start: 0.8853 (p0) cc_final: 0.8619 (p0) REVERT: C 85 SER cc_start: 0.9083 (m) cc_final: 0.8799 (p) REVERT: C 99 GLU cc_start: 0.7234 (pt0) cc_final: 0.6984 (pt0) outliers start: 35 outliers final: 17 residues processed: 189 average time/residue: 0.2004 time to fit residues: 50.8974 Evaluate side-chains 186 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 56 optimal weight: 0.0170 chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS C 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7037 Z= 0.179 Angle : 0.528 10.394 9562 Z= 0.271 Chirality : 0.041 0.143 1022 Planarity : 0.003 0.033 1228 Dihedral : 4.503 28.830 989 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.33 % Allowed : 19.62 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.55 (0.27), residues: 864 helix: -4.71 (0.47), residues: 21 sheet: -1.32 (0.27), residues: 349 loop : -1.83 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 PHE 0.013 0.001 PHE G 377 TYR 0.022 0.001 TYR A 27 ARG 0.006 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 0.772 Fit side-chains REVERT: G 334 ASN cc_start: 0.6727 (p0) cc_final: 0.6506 (p0) REVERT: G 414 GLN cc_start: 0.8094 (mp10) cc_final: 0.7465 (mp10) REVERT: G 440 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8327 (p0) REVERT: G 456 PHE cc_start: 0.7222 (t80) cc_final: 0.6665 (t80) REVERT: G 465 GLU cc_start: 0.7437 (tt0) cc_final: 0.7085 (tp30) REVERT: L 27 GLN cc_start: 0.7524 (mt0) cc_final: 0.7242 (mt0) REVERT: L 83 GLU cc_start: 0.7749 (mp0) cc_final: 0.7516 (mp0) REVERT: B 30 SER cc_start: 0.8638 (t) cc_final: 0.8389 (p) REVERT: B 37 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 19 LYS cc_start: 0.7794 (tttt) cc_final: 0.7431 (tttp) REVERT: A 32 TYR cc_start: 0.8965 (m-80) cc_final: 0.8677 (m-80) REVERT: A 34 MET cc_start: 0.8390 (ttm) cc_final: 0.8014 (ttm) REVERT: A 111 GLN cc_start: 0.8002 (tp40) cc_final: 0.7340 (pm20) REVERT: D 27 ASP cc_start: 0.9018 (t0) cc_final: 0.8592 (t70) REVERT: C 10 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 19 LYS cc_start: 0.7935 (pttt) cc_final: 0.7648 (pptt) REVERT: C 41 HIS cc_start: 0.7645 (t70) cc_final: 0.7157 (t-90) REVERT: C 43 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7818 (mptt) REVERT: C 54 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7944 (p90) REVERT: C 84 ASN cc_start: 0.8861 (p0) cc_final: 0.8625 (p0) REVERT: C 85 SER cc_start: 0.9095 (m) cc_final: 0.8835 (p) REVERT: C 99 GLU cc_start: 0.7152 (pt0) cc_final: 0.6946 (pt0) outliers start: 32 outliers final: 26 residues processed: 191 average time/residue: 0.1731 time to fit residues: 44.4386 Evaluate side-chains 199 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7037 Z= 0.223 Angle : 0.537 7.232 9562 Z= 0.280 Chirality : 0.041 0.146 1022 Planarity : 0.003 0.029 1228 Dihedral : 4.604 29.528 989 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.87 % Allowed : 19.76 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.42 (0.27), residues: 864 helix: -4.74 (0.45), residues: 21 sheet: -1.27 (0.27), residues: 355 loop : -1.70 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 PHE 0.017 0.001 PHE G 377 TYR 0.021 0.001 TYR A 27 ARG 0.006 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 0.729 Fit side-chains REVERT: G 334 ASN cc_start: 0.6942 (p0) cc_final: 0.6674 (p0) REVERT: G 414 GLN cc_start: 0.8130 (mp10) cc_final: 0.7439 (mp10) REVERT: G 440 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8320 (p0) REVERT: G 456 PHE cc_start: 0.7244 (t80) cc_final: 0.6642 (t80) REVERT: G 465 GLU cc_start: 0.7432 (tt0) cc_final: 0.7079 (tp30) REVERT: L 27 GLN cc_start: 0.7503 (mt0) cc_final: 0.7230 (mt0) REVERT: L 83 GLU cc_start: 0.7635 (mp0) cc_final: 0.7403 (mp0) REVERT: H 113 GLN cc_start: 0.7267 (mp10) cc_final: 0.6774 (mp10) REVERT: B 30 SER cc_start: 0.8603 (t) cc_final: 0.8382 (p) REVERT: B 37 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 19 LYS cc_start: 0.7783 (tttt) cc_final: 0.7420 (tttp) REVERT: A 32 TYR cc_start: 0.9029 (m-80) cc_final: 0.8780 (m-80) REVERT: A 34 MET cc_start: 0.8383 (ttm) cc_final: 0.8019 (ttm) REVERT: A 111 GLN cc_start: 0.7997 (tp40) cc_final: 0.7369 (pm20) REVERT: D 4 MET cc_start: 0.8399 (mmm) cc_final: 0.8126 (mmm) REVERT: D 27 ASP cc_start: 0.8994 (t0) cc_final: 0.8688 (t70) REVERT: C 10 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 41 HIS cc_start: 0.7639 (t70) cc_final: 0.7212 (t-90) REVERT: C 43 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7795 (mptt) REVERT: C 54 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8002 (p90) REVERT: C 82 HIS cc_start: 0.7495 (m90) cc_final: 0.7171 (m-70) REVERT: C 84 ASN cc_start: 0.8846 (p0) cc_final: 0.8618 (p0) REVERT: C 85 SER cc_start: 0.9107 (m) cc_final: 0.8843 (p) outliers start: 36 outliers final: 29 residues processed: 192 average time/residue: 0.1740 time to fit residues: 45.1326 Evaluate side-chains 201 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7037 Z= 0.177 Angle : 0.521 7.319 9562 Z= 0.269 Chirality : 0.041 0.142 1022 Planarity : 0.003 0.029 1228 Dihedral : 4.433 30.927 989 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.06 % Allowed : 21.24 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.21 (0.28), residues: 864 helix: -4.58 (0.50), residues: 20 sheet: -1.08 (0.27), residues: 351 loop : -1.61 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 112 HIS 0.006 0.001 HIS B 55 PHE 0.013 0.001 PHE G 392 TYR 0.021 0.001 TYR A 27 ARG 0.007 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 0.717 Fit side-chains REVERT: G 334 ASN cc_start: 0.7068 (p0) cc_final: 0.6765 (p0) REVERT: G 414 GLN cc_start: 0.8046 (mp10) cc_final: 0.7398 (mp10) REVERT: G 440 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8243 (p0) REVERT: G 456 PHE cc_start: 0.7227 (t80) cc_final: 0.6672 (t80) REVERT: L 27 GLN cc_start: 0.7517 (mt0) cc_final: 0.7236 (mt0) REVERT: L 83 GLU cc_start: 0.7635 (mp0) cc_final: 0.7405 (mp0) REVERT: H 82 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6891 (mm-30) REVERT: H 88 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8210 (m) REVERT: H 113 GLN cc_start: 0.7303 (mp10) cc_final: 0.6823 (mp10) REVERT: B 37 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 19 LYS cc_start: 0.7793 (tttt) cc_final: 0.7431 (tttp) REVERT: A 32 TYR cc_start: 0.8981 (m-80) cc_final: 0.8734 (m-80) REVERT: A 34 MET cc_start: 0.8400 (ttm) cc_final: 0.8075 (ttm) REVERT: A 111 GLN cc_start: 0.8001 (tp40) cc_final: 0.7357 (pm20) REVERT: D 4 MET cc_start: 0.8406 (mmm) cc_final: 0.8144 (mmm) REVERT: D 27 ASP cc_start: 0.8996 (t0) cc_final: 0.8691 (t70) REVERT: C 10 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 41 HIS cc_start: 0.7651 (t70) cc_final: 0.7191 (t-90) REVERT: C 43 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7813 (mptt) REVERT: C 54 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8015 (p90) REVERT: C 82 HIS cc_start: 0.7453 (m90) cc_final: 0.7146 (m-70) REVERT: C 84 ASN cc_start: 0.8837 (p0) cc_final: 0.8626 (p0) REVERT: C 85 SER cc_start: 0.9083 (m) cc_final: 0.8823 (p) REVERT: C 99 GLU cc_start: 0.7079 (pt0) cc_final: 0.6852 (pt0) outliers start: 30 outliers final: 24 residues processed: 191 average time/residue: 0.1820 time to fit residues: 46.8620 Evaluate side-chains 201 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 0.0010 chunk 70 optimal weight: 0.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7037 Z= 0.149 Angle : 0.499 7.391 9562 Z= 0.257 Chirality : 0.041 0.137 1022 Planarity : 0.003 0.030 1228 Dihedral : 4.198 29.745 989 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.06 % Allowed : 21.24 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.28), residues: 864 helix: -4.49 (0.52), residues: 20 sheet: -0.99 (0.28), residues: 353 loop : -1.50 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.007 0.001 HIS B 55 PHE 0.011 0.001 PHE G 377 TYR 0.021 0.001 TYR A 27 ARG 0.007 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 0.834 Fit side-chains REVERT: G 334 ASN cc_start: 0.7155 (p0) cc_final: 0.6912 (p0) REVERT: G 376 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7601 (t) REVERT: G 414 GLN cc_start: 0.7972 (mp10) cc_final: 0.7348 (mp10) REVERT: G 440 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8223 (p0) REVERT: G 456 PHE cc_start: 0.7192 (t80) cc_final: 0.6600 (t80) REVERT: L 27 GLN cc_start: 0.7502 (mt0) cc_final: 0.7226 (mt0) REVERT: L 60 CYS cc_start: 0.8501 (t) cc_final: 0.8194 (p) REVERT: L 83 GLU cc_start: 0.7632 (mp0) cc_final: 0.7408 (mp0) REVERT: H 10 GLU cc_start: 0.7073 (tp30) cc_final: 0.6794 (mm-30) REVERT: H 82 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6889 (mm-30) REVERT: H 88 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8284 (m) REVERT: H 113 GLN cc_start: 0.7319 (mp10) cc_final: 0.6837 (mp10) REVERT: B 37 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 19 LYS cc_start: 0.7780 (tttt) cc_final: 0.7421 (tttp) REVERT: A 32 TYR cc_start: 0.8980 (m-80) cc_final: 0.8706 (m-80) REVERT: A 34 MET cc_start: 0.8413 (ttm) cc_final: 0.8083 (ttm) REVERT: A 74 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6872 (mtmm) REVERT: A 111 GLN cc_start: 0.8012 (tp40) cc_final: 0.7365 (pm20) REVERT: D 61 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7067 (mtm-85) REVERT: C 7 SER cc_start: 0.7636 (t) cc_final: 0.7221 (p) REVERT: C 10 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 41 HIS cc_start: 0.7651 (t70) cc_final: 0.7188 (t-90) REVERT: C 43 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7834 (mptt) REVERT: C 82 HIS cc_start: 0.7456 (m90) cc_final: 0.7235 (m-70) REVERT: C 85 SER cc_start: 0.9070 (m) cc_final: 0.8838 (p) REVERT: C 98 LYS cc_start: 0.6529 (pptt) cc_final: 0.6280 (pptt) REVERT: C 99 GLU cc_start: 0.7043 (pt0) cc_final: 0.6817 (pt0) outliers start: 30 outliers final: 23 residues processed: 197 average time/residue: 0.1853 time to fit residues: 48.2959 Evaluate side-chains 194 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7037 Z= 0.238 Angle : 0.550 7.737 9562 Z= 0.286 Chirality : 0.042 0.145 1022 Planarity : 0.003 0.030 1228 Dihedral : 4.473 31.543 989 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.65 % Allowed : 21.92 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.01 (0.28), residues: 864 helix: -4.88 (0.42), residues: 20 sheet: -0.92 (0.27), residues: 363 loop : -1.47 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 PHE 0.018 0.001 PHE G 377 TYR 0.026 0.001 TYR H 80 ARG 0.007 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 334 ASN cc_start: 0.7259 (p0) cc_final: 0.6976 (p0) REVERT: G 414 GLN cc_start: 0.8107 (mp10) cc_final: 0.7374 (mp10) REVERT: L 27 GLN cc_start: 0.7495 (mt0) cc_final: 0.7225 (mt0) REVERT: L 60 CYS cc_start: 0.8503 (t) cc_final: 0.8239 (p) REVERT: L 83 GLU cc_start: 0.7587 (mp0) cc_final: 0.7303 (mp0) REVERT: H 88 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8234 (m) REVERT: H 113 GLN cc_start: 0.7302 (mp10) cc_final: 0.6856 (mp10) REVERT: B 4 MET cc_start: 0.6459 (mmm) cc_final: 0.5888 (ttm) REVERT: B 37 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 19 LYS cc_start: 0.7795 (tttt) cc_final: 0.7433 (tttp) REVERT: A 32 TYR cc_start: 0.9036 (m-80) cc_final: 0.8800 (m-80) REVERT: A 34 MET cc_start: 0.8401 (ttm) cc_final: 0.8082 (ttm) REVERT: A 74 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6914 (mtmm) REVERT: A 111 GLN cc_start: 0.7998 (tp40) cc_final: 0.7386 (pm20) REVERT: D 4 MET cc_start: 0.8433 (mmm) cc_final: 0.8199 (mmm) REVERT: C 10 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 41 HIS cc_start: 0.7648 (t70) cc_final: 0.7190 (t-90) REVERT: C 43 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7836 (mptt) REVERT: C 82 HIS cc_start: 0.7625 (m90) cc_final: 0.7345 (m-70) REVERT: C 85 SER cc_start: 0.9159 (m) cc_final: 0.8930 (p) outliers start: 27 outliers final: 25 residues processed: 175 average time/residue: 0.1802 time to fit residues: 41.7667 Evaluate side-chains 188 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7037 Z= 0.201 Angle : 0.530 7.885 9562 Z= 0.275 Chirality : 0.042 0.141 1022 Planarity : 0.003 0.028 1228 Dihedral : 4.384 30.684 989 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.19 % Allowed : 21.52 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.96 (0.28), residues: 864 helix: -4.80 (0.47), residues: 20 sheet: -0.89 (0.27), residues: 355 loop : -1.45 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 112 HIS 0.008 0.001 HIS B 55 PHE 0.015 0.001 PHE G 377 TYR 0.028 0.001 TYR H 80 ARG 0.009 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: G 334 ASN cc_start: 0.7355 (p0) cc_final: 0.7036 (p0) REVERT: G 414 GLN cc_start: 0.8126 (mp10) cc_final: 0.7359 (mp10) REVERT: L 27 GLN cc_start: 0.7505 (mt0) cc_final: 0.7237 (mt0) REVERT: L 60 CYS cc_start: 0.8454 (t) cc_final: 0.8204 (p) REVERT: L 83 GLU cc_start: 0.7545 (mp0) cc_final: 0.7324 (mp0) REVERT: H 88 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8294 (m) REVERT: H 113 GLN cc_start: 0.7314 (mp10) cc_final: 0.6825 (mp10) REVERT: B 4 MET cc_start: 0.6492 (mmm) cc_final: 0.5956 (ttm) REVERT: B 37 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 19 LYS cc_start: 0.7773 (tttt) cc_final: 0.7418 (tttp) REVERT: A 32 TYR cc_start: 0.9035 (m-80) cc_final: 0.8792 (m-80) REVERT: A 34 MET cc_start: 0.8369 (ttm) cc_final: 0.8016 (ttm) REVERT: A 74 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6887 (mtmm) REVERT: A 111 GLN cc_start: 0.8015 (tp40) cc_final: 0.7394 (pm20) REVERT: C 10 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 41 HIS cc_start: 0.7654 (t70) cc_final: 0.7202 (t-90) REVERT: C 43 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7836 (mptt) REVERT: C 82 HIS cc_start: 0.7588 (m90) cc_final: 0.6867 (m-70) outliers start: 31 outliers final: 28 residues processed: 182 average time/residue: 0.1904 time to fit residues: 45.8092 Evaluate side-chains 192 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102331 restraints weight = 10992.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105387 restraints weight = 6855.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107488 restraints weight = 5081.435| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7037 Z= 0.163 Angle : 0.529 9.550 9562 Z= 0.272 Chirality : 0.041 0.136 1022 Planarity : 0.003 0.029 1228 Dihedral : 4.201 29.693 989 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.79 % Allowed : 21.79 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.94 (0.28), residues: 864 helix: -4.78 (0.47), residues: 20 sheet: -0.90 (0.27), residues: 359 loop : -1.41 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.008 0.001 HIS B 55 PHE 0.011 0.001 PHE G 377 TYR 0.025 0.001 TYR H 80 ARG 0.009 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.94 seconds wall clock time: 42 minutes 58.28 seconds (2578.28 seconds total)