Starting phenix.real_space_refine on Mon Mar 11 18:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1f_23109/03_2024/7l1f_23109_updated.pdb" } resolution = 3.89 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 ------------------------------------------------------------------------------- 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= 0.021 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 58 5.16 5 C 5504 2.51 5 N 1473 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8825 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6708 Classifications: {'peptide': 832} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 803} Chain breaks: 3 Chain: "C" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 486 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 372 Unusual residues: {'F86': 4} Classifications: {'RNA': 13, 'undetermined': 4} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12, None: 4} Not linked: pdbres=" U P 13 " pdbres="F86 P 14 " Not linked: pdbres="F86 P 14 " pdbres="F86 P 15 " Not linked: pdbres="F86 P 15 " pdbres="F86 P 16 " Not linked: pdbres="F86 P 16 " pdbres="F86 P 17 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Chain: "T" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 376 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 16} Time building chain proxies: 5.49, per 1000 atoms: 0.62 Number of scatterers: 8825 At special positions: 0 Unit cell: (86.9, 99, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 35 15.00 O 1755 8.00 N 1473 7.00 C 5504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 6 sheets defined 40.1% alpha, 5.1% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.108A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 187 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 194 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.335A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 306 through 319 removed outlier: 4.432A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 417 through 423 Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.163A pdb=" N ALA A 449 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 455 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.978A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.015A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.663A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 removed outlier: 4.233A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 865 removed outlier: 5.102A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 918 through 924 removed outlier: 3.613A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 117 through 124 Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.731A pdb=" N GLN D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 removed outlier: 3.874A pdb=" N GLN D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 61 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.524A pdb=" N ALA A 46 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.806A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= D, first strand: chain 'A' and resid 612 through 614 removed outlier: 3.818A pdb=" N HIS A 613 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 761 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 removed outlier: 3.767A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.016A pdb=" N LEU C 128 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 130 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 147 " --> pdb=" O TRP C 154 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1364 1.27 - 1.41: 2436 1.41 - 1.55: 5044 1.55 - 1.68: 162 1.68 - 1.82: 87 Bond restraints: 9093 Sorted by residual: bond pdb=" C11 F86 P 15 " pdb=" N5 F86 P 15 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.00e-02 1.00e+04 1.37e+02 bond pdb=" C11 F86 P 16 " pdb=" N5 F86 P 16 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.00e-02 1.00e+04 1.32e+02 bond pdb=" C11 F86 P 14 " pdb=" N5 F86 P 14 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C11 F86 P 17 " pdb=" N5 F86 P 17 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C12 F86 P 15 " pdb=" N2 F86 P 15 " ideal model delta sigma weight residual 1.293 1.358 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 9088 not shown) Histogram of bond angle deviations from ideal: 96.05 - 112.74: 4727 112.74 - 129.44: 7685 129.44 - 146.13: 81 146.13 - 162.83: 0 162.83 - 179.52: 4 Bond angle restraints: 12497 Sorted by residual: angle pdb=" C THR A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta sigma weight residual 121.97 137.48 -15.51 1.80e+00 3.09e-01 7.42e+01 angle pdb=" C TRP C 182 " pdb=" N PRO C 183 " pdb=" CD PRO C 183 " ideal model delta sigma weight residual 120.60 104.96 15.64 2.20e+00 2.07e-01 5.06e+01 angle pdb=" CB LYS A 411 " pdb=" CG LYS A 411 " pdb=" CD LYS A 411 " ideal model delta sigma weight residual 111.30 127.43 -16.13 2.30e+00 1.89e-01 4.92e+01 angle pdb=" C7 F86 P 16 " pdb=" C5 F86 P 16 " pdb=" N1 F86 P 16 " ideal model delta sigma weight residual 107.20 113.84 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP A 304 " pdb=" CB ASP A 304 " pdb=" CG ASP A 304 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.28e+01 ... (remaining 12492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5007 23.49 - 46.97: 311 46.97 - 70.46: 44 70.46 - 93.94: 8 93.94 - 117.43: 1 Dihedral angle restraints: 5371 sinusoidal: 2378 harmonic: 2993 Sorted by residual: dihedral pdb=" CA THR A 556 " pdb=" C THR A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA LEU C 98 " pdb=" C LEU C 98 " pdb=" N ASP C 99 " pdb=" CA ASP C 99 " ideal model delta harmonic sigma weight residual -180.00 -149.78 -30.22 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA ALA A 762 " pdb=" C ALA A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 5368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1257 0.105 - 0.210: 138 0.210 - 0.315: 26 0.315 - 0.419: 3 0.419 - 0.524: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB VAL A 588 " pdb=" CA VAL A 588 " pdb=" CG1 VAL A 588 " pdb=" CG2 VAL A 588 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CB THR A 556 " pdb=" CA THR A 556 " pdb=" OG1 THR A 556 " pdb=" CG2 THR A 556 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB VAL A 476 " pdb=" CA VAL A 476 " pdb=" CG1 VAL A 476 " pdb=" CG2 VAL A 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 1423 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 157 " 0.021 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE A 157 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 157 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 157 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 157 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.007 2.00e-02 2.50e+03 2.84e-02 1.62e+01 pdb=" CG TYR A 237 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 182 " 0.060 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO C 183 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " 0.034 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2811 2.84 - 3.35: 7290 3.35 - 3.87: 14471 3.87 - 4.38: 15694 4.38 - 4.90: 25853 Nonbonded interactions: 66119 Sorted by model distance: nonbonded pdb=" OG1 THR A 540 " pdb=" OE2 GLU A 665 " model vdw 2.323 2.440 nonbonded pdb=" OG1 THR A 246 " pdb=" O PRO A 461 " model vdw 2.330 2.440 nonbonded pdb=" O THR C 89 " pdb=" OG1 THR C 93 " model vdw 2.344 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.349 2.440 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.349 2.440 ... (remaining 66114 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=0.00 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: 0.030 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.940 Find NCS groups from input model: 0.210 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.008 0.117 9093 Z= 0.503 Angle : 1.362 16.168 12497 Z= 0.737 Chirality : 0.075 0.524 1426 Planarity : 0.008 0.087 1466 Dihedral : 14.821 117.425 3439 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.38 (0.20), residues: 997 helix: -3.54 (0.15), residues: 411 sheet: -2.04 (0.65), residues: 61 loop : -2.45 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 29 HIS 0.017 0.002 HIS A 309 PHE 0.069 0.004 PHE A 157 TYR 0.064 0.004 TYR A 237 ARG 0.025 0.002 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7376 (tpt) cc_final: 0.6950 (tpt) REVERT: A 143 LYS cc_start: 0.7914 (tppp) cc_final: 0.7662 (tptt) REVERT: A 149 TYR cc_start: 0.8083 (m-80) cc_final: 0.7788 (m-10) REVERT: A 150 ASN cc_start: 0.7788 (m110) cc_final: 0.7513 (m110) REVERT: A 173 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7815 (ttp80) REVERT: A 283 PHE cc_start: 0.7485 (t80) cc_final: 0.7060 (t80) REVERT: A 395 CYS cc_start: 0.7589 (m) cc_final: 0.7324 (m) REVERT: A 454 ASP cc_start: 0.7414 (t0) cc_final: 0.6994 (t0) REVERT: A 691 ASN cc_start: 0.8311 (m110) cc_final: 0.8036 (m-40) REVERT: A 698 GLN cc_start: 0.7715 (mp10) cc_final: 0.7507 (mp10) REVERT: A 703 ASN cc_start: 0.8006 (m-40) cc_final: 0.7563 (m-40) REVERT: A 707 LEU cc_start: 0.8546 (tp) cc_final: 0.8315 (tp) REVERT: A 748 TYR cc_start: 0.7782 (t80) cc_final: 0.7476 (t80) REVERT: A 815 GLN cc_start: 0.7505 (mm110) cc_final: 0.7223 (mm110) REVERT: A 855 MET cc_start: 0.6818 (mtm) cc_final: 0.6117 (mtm) REVERT: A 857 GLU cc_start: 0.7442 (pm20) cc_final: 0.7214 (pm20) REVERT: A 892 HIS cc_start: 0.7798 (t70) cc_final: 0.7535 (t70) REVERT: C 129 MET cc_start: 0.6852 (ppp) cc_final: 0.6571 (ppp) REVERT: C 157 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8211 (tm-30) REVERT: D 2 LYS cc_start: 0.6639 (pttp) cc_final: 0.6289 (pttm) REVERT: D 51 LYS cc_start: 0.7629 (mptt) cc_final: 0.7409 (tptt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2322 time to fit residues: 78.5765 Evaluate side-chains 215 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9093 Z= 0.280 Angle : 0.669 7.175 12497 Z= 0.361 Chirality : 0.044 0.228 1426 Planarity : 0.005 0.079 1466 Dihedral : 12.325 125.894 1567 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.24 % Allowed : 10.21 % Favored : 87.54 % 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: -3.18 (0.22), residues: 997 helix: -1.76 (0.21), residues: 429 sheet: -2.66 (0.53), residues: 77 loop : -2.30 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 154 HIS 0.006 0.001 HIS D 36 PHE 0.036 0.002 PHE A 157 TYR 0.023 0.002 TYR A 273 ARG 0.006 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7580 (tpt) cc_final: 0.6902 (tpt) REVERT: A 150 ASN cc_start: 0.8023 (m110) cc_final: 0.7655 (m110) REVERT: A 167 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 242 MET cc_start: 0.7345 (mtp) cc_final: 0.6875 (mtp) REVERT: A 365 ARG cc_start: 0.7465 (mtt90) cc_final: 0.7256 (mtt90) REVERT: A 395 CYS cc_start: 0.7543 (m) cc_final: 0.7317 (m) REVERT: A 454 ASP cc_start: 0.7640 (t0) cc_final: 0.7239 (t0) REVERT: A 463 MET cc_start: 0.6292 (ppp) cc_final: 0.5951 (ppp) REVERT: A 466 ILE cc_start: 0.7644 (tp) cc_final: 0.6945 (mm) REVERT: A 661 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7228 (mm-40) REVERT: A 703 ASN cc_start: 0.8182 (m110) cc_final: 0.7682 (m110) REVERT: A 765 CYS cc_start: 0.8515 (t) cc_final: 0.8225 (t) REVERT: A 766 PHE cc_start: 0.8707 (p90) cc_final: 0.7909 (p90) REVERT: A 782 PHE cc_start: 0.7508 (m-80) cc_final: 0.6986 (t80) REVERT: A 855 MET cc_start: 0.6876 (mtm) cc_final: 0.6209 (mtm) REVERT: A 889 ARG cc_start: 0.7608 (tmm160) cc_final: 0.7103 (tmm160) REVERT: A 892 HIS cc_start: 0.7870 (t70) cc_final: 0.7661 (t70) REVERT: A 919 GLU cc_start: 0.7787 (mp0) cc_final: 0.7397 (mp0) REVERT: A 924 MET cc_start: 0.7439 (tpp) cc_final: 0.7071 (ttm) REVERT: C 129 MET cc_start: 0.6815 (ppp) cc_final: 0.6343 (ppp) REVERT: C 157 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 2 LYS cc_start: 0.6457 (pttp) cc_final: 0.5908 (pttm) REVERT: D 7 LYS cc_start: 0.7746 (mttm) cc_final: 0.7521 (mttp) REVERT: D 51 LYS cc_start: 0.7587 (mptt) cc_final: 0.7377 (tptt) outliers start: 20 outliers final: 17 residues processed: 234 average time/residue: 0.2357 time to fit residues: 73.8434 Evaluate side-chains 238 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.0870 chunk 62 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9093 Z= 0.139 Angle : 0.552 8.290 12497 Z= 0.291 Chirality : 0.040 0.165 1426 Planarity : 0.004 0.041 1466 Dihedral : 11.818 125.618 1567 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.69 % Allowed : 13.24 % Favored : 84.06 % 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: -2.44 (0.24), residues: 997 helix: -0.99 (0.24), residues: 431 sheet: -2.18 (0.56), residues: 71 loop : -2.09 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 268 HIS 0.002 0.000 HIS A 309 PHE 0.025 0.001 PHE A 415 TYR 0.012 0.001 TYR C 149 ARG 0.007 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7738 (mttt) cc_final: 0.7274 (mttm) REVERT: A 124 MET cc_start: 0.7541 (tpt) cc_final: 0.7216 (tpt) REVERT: A 150 ASN cc_start: 0.7836 (m110) cc_final: 0.7512 (m110) REVERT: A 183 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7730 (ttm170) REVERT: A 242 MET cc_start: 0.7193 (mtp) cc_final: 0.6837 (mtp) REVERT: A 365 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7136 (mtt90) REVERT: A 380 MET cc_start: 0.7221 (tmm) cc_final: 0.7001 (tmm) REVERT: A 395 CYS cc_start: 0.7543 (m) cc_final: 0.7320 (m) REVERT: A 454 ASP cc_start: 0.7563 (t0) cc_final: 0.7151 (t0) REVERT: A 463 MET cc_start: 0.6209 (ppp) cc_final: 0.5921 (ppp) REVERT: A 466 ILE cc_start: 0.7612 (tp) cc_final: 0.7036 (mm) REVERT: A 571 PHE cc_start: 0.7928 (t80) cc_final: 0.7665 (t80) REVERT: A 645 CYS cc_start: 0.8207 (m) cc_final: 0.6983 (t) REVERT: A 698 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8216 (mm-40) REVERT: A 703 ASN cc_start: 0.8141 (m110) cc_final: 0.7679 (m110) REVERT: A 765 CYS cc_start: 0.8444 (t) cc_final: 0.7950 (t) REVERT: A 766 PHE cc_start: 0.8671 (p90) cc_final: 0.7967 (p90) REVERT: A 782 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6843 (t80) REVERT: A 819 LEU cc_start: 0.8573 (tp) cc_final: 0.8081 (tp) REVERT: A 855 MET cc_start: 0.6730 (mtm) cc_final: 0.5987 (mtm) REVERT: A 881 PHE cc_start: 0.7838 (t80) cc_final: 0.7565 (t80) REVERT: A 889 ARG cc_start: 0.7623 (tmm160) cc_final: 0.6986 (tmm160) REVERT: A 919 GLU cc_start: 0.7512 (mp0) cc_final: 0.7308 (mp0) REVERT: A 924 MET cc_start: 0.7357 (tpp) cc_final: 0.6981 (ttm) REVERT: C 117 LEU cc_start: 0.7997 (tt) cc_final: 0.7729 (tt) REVERT: C 129 MET cc_start: 0.6601 (ppp) cc_final: 0.6313 (ppp) REVERT: C 157 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 51 LYS cc_start: 0.7578 (mptt) cc_final: 0.7366 (tptt) outliers start: 24 outliers final: 17 residues processed: 234 average time/residue: 0.2250 time to fit residues: 71.4765 Evaluate side-chains 241 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain D residue 3 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 0.0570 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9093 Z= 0.211 Angle : 0.578 6.997 12497 Z= 0.307 Chirality : 0.042 0.277 1426 Planarity : 0.004 0.050 1466 Dihedral : 11.733 127.428 1567 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.70 % Allowed : 15.26 % Favored : 81.03 % 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: -2.08 (0.24), residues: 997 helix: -0.54 (0.25), residues: 429 sheet: -2.31 (0.55), residues: 71 loop : -2.00 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 29 HIS 0.004 0.001 HIS D 36 PHE 0.026 0.002 PHE A 415 TYR 0.017 0.001 TYR A 273 ARG 0.008 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7613 (tpt) cc_final: 0.7293 (tpt) REVERT: A 150 ASN cc_start: 0.7845 (m110) cc_final: 0.7546 (m110) REVERT: A 248 THR cc_start: 0.8821 (p) cc_final: 0.8614 (t) REVERT: A 249 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7418 (ttm-80) REVERT: A 347 HIS cc_start: 0.7940 (t-90) cc_final: 0.7730 (t-90) REVERT: A 365 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7208 (mtt90) REVERT: A 380 MET cc_start: 0.7414 (tmm) cc_final: 0.7171 (tmm) REVERT: A 395 CYS cc_start: 0.7388 (m) cc_final: 0.7163 (m) REVERT: A 454 ASP cc_start: 0.7696 (t0) cc_final: 0.7258 (t0) REVERT: A 463 MET cc_start: 0.6331 (ppp) cc_final: 0.5909 (ppp) REVERT: A 466 ILE cc_start: 0.7642 (tp) cc_final: 0.7355 (mm) REVERT: A 609 VAL cc_start: 0.7736 (m) cc_final: 0.7435 (t) REVERT: A 645 CYS cc_start: 0.8261 (m) cc_final: 0.6660 (t) REVERT: A 698 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8111 (mm-40) REVERT: A 703 ASN cc_start: 0.8230 (m110) cc_final: 0.7806 (m110) REVERT: A 765 CYS cc_start: 0.8445 (t) cc_final: 0.7995 (t) REVERT: A 782 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6909 (t80) REVERT: A 855 MET cc_start: 0.6796 (mtm) cc_final: 0.5986 (mtm) REVERT: A 881 PHE cc_start: 0.7802 (t80) cc_final: 0.7503 (t80) REVERT: A 886 GLN cc_start: 0.7698 (mm-40) cc_final: 0.6389 (mp10) REVERT: A 889 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7030 (tmm160) REVERT: A 917 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 919 GLU cc_start: 0.7850 (mp0) cc_final: 0.7274 (mp0) REVERT: A 924 MET cc_start: 0.7291 (tpp) cc_final: 0.6909 (ttm) REVERT: C 129 MET cc_start: 0.6744 (ppp) cc_final: 0.6282 (ppp) REVERT: C 157 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 33 outliers final: 27 residues processed: 237 average time/residue: 0.2110 time to fit residues: 68.2957 Evaluate side-chains 253 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9093 Z= 0.162 Angle : 0.552 7.058 12497 Z= 0.289 Chirality : 0.041 0.301 1426 Planarity : 0.004 0.051 1466 Dihedral : 11.567 124.923 1567 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.14 % Allowed : 17.73 % Favored : 79.12 % 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: -1.79 (0.25), residues: 997 helix: -0.19 (0.25), residues: 424 sheet: -2.46 (0.52), residues: 73 loop : -1.88 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 29 HIS 0.003 0.001 HIS D 36 PHE 0.025 0.001 PHE A 415 TYR 0.021 0.001 TYR A 689 ARG 0.009 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7678 (tpt) cc_final: 0.7315 (tpt) REVERT: A 150 ASN cc_start: 0.7892 (m110) cc_final: 0.7558 (m110) REVERT: A 242 MET cc_start: 0.7277 (mtp) cc_final: 0.6952 (mtp) REVERT: A 249 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7532 (ttm-80) REVERT: A 331 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6730 (tpp80) REVERT: A 347 HIS cc_start: 0.7905 (t-90) cc_final: 0.7698 (t-90) REVERT: A 365 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7191 (mtt90) REVERT: A 380 MET cc_start: 0.7386 (tmm) cc_final: 0.7184 (tmm) REVERT: A 395 CYS cc_start: 0.7428 (m) cc_final: 0.7204 (m) REVERT: A 454 ASP cc_start: 0.7666 (t0) cc_final: 0.7209 (t0) REVERT: A 463 MET cc_start: 0.6406 (ppp) cc_final: 0.6080 (ppp) REVERT: A 466 ILE cc_start: 0.7619 (tp) cc_final: 0.6999 (mm) REVERT: A 645 CYS cc_start: 0.8227 (m) cc_final: 0.6679 (t) REVERT: A 698 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8103 (mm-40) REVERT: A 703 ASN cc_start: 0.8126 (m110) cc_final: 0.7658 (m110) REVERT: A 729 GLU cc_start: 0.7736 (tp30) cc_final: 0.7415 (tp30) REVERT: A 765 CYS cc_start: 0.8411 (t) cc_final: 0.7850 (t) REVERT: A 782 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 855 MET cc_start: 0.6760 (mtm) cc_final: 0.5919 (mtm) REVERT: A 889 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7001 (tmm160) REVERT: A 917 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 919 GLU cc_start: 0.7872 (mp0) cc_final: 0.7295 (mp0) REVERT: C 129 MET cc_start: 0.6682 (ppp) cc_final: 0.6304 (ppp) REVERT: C 157 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8012 (tm-30) outliers start: 28 outliers final: 23 residues processed: 238 average time/residue: 0.2097 time to fit residues: 67.9159 Evaluate side-chains 246 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 0.0770 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9093 Z= 0.217 Angle : 0.588 10.538 12497 Z= 0.305 Chirality : 0.042 0.288 1426 Planarity : 0.004 0.056 1466 Dihedral : 11.582 124.804 1567 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.82 % Allowed : 17.85 % Favored : 78.34 % 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: -1.67 (0.25), residues: 997 helix: -0.05 (0.26), residues: 421 sheet: -2.54 (0.51), residues: 73 loop : -1.82 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 29 HIS 0.004 0.001 HIS D 36 PHE 0.023 0.002 PHE A 415 TYR 0.018 0.001 TYR A 689 ARG 0.007 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7684 (mttt) cc_final: 0.7170 (mttm) REVERT: A 124 MET cc_start: 0.7712 (tpt) cc_final: 0.7405 (tpt) REVERT: A 150 ASN cc_start: 0.7832 (m110) cc_final: 0.7501 (m110) REVERT: A 242 MET cc_start: 0.7438 (mtp) cc_final: 0.6988 (mtp) REVERT: A 331 ARG cc_start: 0.7220 (tpp80) cc_final: 0.6811 (tpp80) REVERT: A 365 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7219 (mtt90) REVERT: A 380 MET cc_start: 0.7445 (tmm) cc_final: 0.7211 (tmm) REVERT: A 395 CYS cc_start: 0.7571 (m) cc_final: 0.7324 (m) REVERT: A 454 ASP cc_start: 0.7743 (t0) cc_final: 0.7288 (t0) REVERT: A 463 MET cc_start: 0.6392 (ppp) cc_final: 0.5993 (ppp) REVERT: A 466 ILE cc_start: 0.7618 (tp) cc_final: 0.7076 (mm) REVERT: A 609 VAL cc_start: 0.7684 (m) cc_final: 0.7357 (t) REVERT: A 645 CYS cc_start: 0.8218 (m) cc_final: 0.6645 (t) REVERT: A 698 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8078 (mm-40) REVERT: A 703 ASN cc_start: 0.8330 (m110) cc_final: 0.7862 (m110) REVERT: A 729 GLU cc_start: 0.7849 (tp30) cc_final: 0.7623 (tp30) REVERT: A 765 CYS cc_start: 0.8426 (t) cc_final: 0.7950 (t) REVERT: A 782 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6922 (t80) REVERT: A 855 MET cc_start: 0.6723 (mtm) cc_final: 0.5950 (mtm) REVERT: A 881 PHE cc_start: 0.7721 (t80) cc_final: 0.7494 (t80) REVERT: A 889 ARG cc_start: 0.7699 (tmm160) cc_final: 0.7039 (tmm160) REVERT: A 919 GLU cc_start: 0.7895 (mp0) cc_final: 0.7295 (mp0) REVERT: C 129 MET cc_start: 0.6783 (ppp) cc_final: 0.6323 (ppp) REVERT: C 157 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8036 (tm-30) outliers start: 34 outliers final: 29 residues processed: 235 average time/residue: 0.2085 time to fit residues: 66.8411 Evaluate side-chains 251 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9093 Z= 0.307 Angle : 0.645 9.108 12497 Z= 0.341 Chirality : 0.045 0.288 1426 Planarity : 0.004 0.060 1466 Dihedral : 11.714 122.451 1567 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.82 % Allowed : 20.09 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.78 (0.25), residues: 997 helix: -0.14 (0.26), residues: 411 sheet: -3.00 (0.47), residues: 79 loop : -1.75 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 29 HIS 0.005 0.001 HIS D 36 PHE 0.022 0.002 PHE A 157 TYR 0.023 0.002 TYR A 273 ARG 0.006 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7761 (mttt) cc_final: 0.7189 (mttm) REVERT: A 124 MET cc_start: 0.7687 (tpt) cc_final: 0.6947 (tpt) REVERT: A 150 ASN cc_start: 0.7916 (m110) cc_final: 0.7582 (m110) REVERT: A 242 MET cc_start: 0.7487 (mtp) cc_final: 0.7069 (mtp) REVERT: A 294 TYR cc_start: 0.8009 (t80) cc_final: 0.7716 (t80) REVERT: A 365 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7253 (mtt90) REVERT: A 380 MET cc_start: 0.7508 (tmm) cc_final: 0.7269 (tmm) REVERT: A 395 CYS cc_start: 0.7621 (m) cc_final: 0.7365 (m) REVERT: A 454 ASP cc_start: 0.7788 (t0) cc_final: 0.7418 (t0) REVERT: A 463 MET cc_start: 0.6472 (ppp) cc_final: 0.5999 (ppp) REVERT: A 466 ILE cc_start: 0.7643 (tp) cc_final: 0.7102 (mm) REVERT: A 645 CYS cc_start: 0.8261 (m) cc_final: 0.6652 (t) REVERT: A 698 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8073 (mm-40) REVERT: A 703 ASN cc_start: 0.8320 (m110) cc_final: 0.7857 (m110) REVERT: A 729 GLU cc_start: 0.7993 (tp30) cc_final: 0.7699 (tp30) REVERT: A 734 ASN cc_start: 0.7991 (m-40) cc_final: 0.7660 (t0) REVERT: A 765 CYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8022 (t) REVERT: A 782 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 855 MET cc_start: 0.6832 (mtm) cc_final: 0.6126 (mtm) REVERT: A 886 GLN cc_start: 0.7774 (mm-40) cc_final: 0.6474 (mm-40) REVERT: A 889 ARG cc_start: 0.7728 (tmm160) cc_final: 0.7106 (tmm160) REVERT: C 129 MET cc_start: 0.6839 (ppp) cc_final: 0.6289 (ppp) outliers start: 34 outliers final: 31 residues processed: 235 average time/residue: 0.2096 time to fit residues: 67.8317 Evaluate side-chains 256 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 642 HIS C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9093 Z= 0.149 Angle : 0.569 10.856 12497 Z= 0.293 Chirality : 0.041 0.246 1426 Planarity : 0.004 0.054 1466 Dihedral : 11.407 117.322 1567 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.48 % Allowed : 21.44 % Favored : 75.08 % 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: -1.53 (0.25), residues: 997 helix: 0.02 (0.26), residues: 424 sheet: -1.95 (0.53), residues: 69 loop : -1.81 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 29 HIS 0.002 0.000 HIS A 816 PHE 0.029 0.001 PHE A 812 TYR 0.015 0.001 TYR A 689 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7673 (mttt) cc_final: 0.7241 (mttm) REVERT: A 124 MET cc_start: 0.7630 (tpt) cc_final: 0.7245 (tpt) REVERT: A 150 ASN cc_start: 0.7819 (m110) cc_final: 0.7517 (m110) REVERT: A 242 MET cc_start: 0.7277 (mtp) cc_final: 0.6773 (mtp) REVERT: A 365 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7196 (mtt90) REVERT: A 395 CYS cc_start: 0.7567 (m) cc_final: 0.7331 (m) REVERT: A 454 ASP cc_start: 0.7728 (t0) cc_final: 0.7319 (t0) REVERT: A 463 MET cc_start: 0.6390 (ppp) cc_final: 0.5931 (ppp) REVERT: A 466 ILE cc_start: 0.7590 (tp) cc_final: 0.7044 (mm) REVERT: A 645 CYS cc_start: 0.8175 (m) cc_final: 0.6657 (t) REVERT: A 689 TYR cc_start: 0.7817 (m-80) cc_final: 0.7533 (m-80) REVERT: A 698 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8061 (mm-40) REVERT: A 703 ASN cc_start: 0.8150 (m110) cc_final: 0.7661 (m110) REVERT: A 718 LYS cc_start: 0.8170 (tppt) cc_final: 0.7865 (tptt) REVERT: A 729 GLU cc_start: 0.7900 (tp30) cc_final: 0.7611 (tp30) REVERT: A 734 ASN cc_start: 0.7966 (m-40) cc_final: 0.7635 (t0) REVERT: A 765 CYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7760 (t) REVERT: A 782 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6837 (t80) REVERT: A 807 LYS cc_start: 0.8732 (pttm) cc_final: 0.8507 (pttm) REVERT: A 818 MET cc_start: 0.7320 (ppp) cc_final: 0.6578 (ppp) REVERT: A 819 LEU cc_start: 0.8023 (tp) cc_final: 0.6875 (mt) REVERT: A 855 MET cc_start: 0.6719 (mtm) cc_final: 0.6017 (mtm) REVERT: A 886 GLN cc_start: 0.7669 (mm-40) cc_final: 0.6256 (mm-40) REVERT: A 889 ARG cc_start: 0.7700 (tmm160) cc_final: 0.6950 (tmm160) REVERT: C 129 MET cc_start: 0.6719 (ppp) cc_final: 0.6347 (ppp) REVERT: C 157 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 7 LYS cc_start: 0.7641 (mttm) cc_final: 0.7301 (mttp) outliers start: 31 outliers final: 25 residues processed: 236 average time/residue: 0.2125 time to fit residues: 68.5417 Evaluate side-chains 254 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9093 Z= 0.198 Angle : 0.592 10.182 12497 Z= 0.306 Chirality : 0.042 0.251 1426 Planarity : 0.004 0.058 1466 Dihedral : 11.443 118.692 1567 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.59 % Allowed : 21.44 % Favored : 74.97 % 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: -1.38 (0.26), residues: 997 helix: 0.16 (0.26), residues: 416 sheet: -1.95 (0.53), residues: 69 loop : -1.70 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 29 HIS 0.004 0.001 HIS A 381 PHE 0.020 0.001 PHE A 415 TYR 0.015 0.001 TYR A 689 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 225 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7683 (mttt) cc_final: 0.7082 (mmtt) REVERT: A 124 MET cc_start: 0.7688 (tpt) cc_final: 0.7298 (tpt) REVERT: A 150 ASN cc_start: 0.7874 (m110) cc_final: 0.7564 (m110) REVERT: A 242 MET cc_start: 0.7416 (mtp) cc_final: 0.6921 (mtp) REVERT: A 365 ARG cc_start: 0.7478 (mtt90) cc_final: 0.7231 (mtt90) REVERT: A 395 CYS cc_start: 0.7575 (m) cc_final: 0.7353 (m) REVERT: A 454 ASP cc_start: 0.7759 (t0) cc_final: 0.7376 (t0) REVERT: A 463 MET cc_start: 0.6392 (ppp) cc_final: 0.5926 (ppp) REVERT: A 466 ILE cc_start: 0.7607 (tp) cc_final: 0.7068 (mm) REVERT: A 645 CYS cc_start: 0.8152 (m) cc_final: 0.6616 (t) REVERT: A 689 TYR cc_start: 0.7869 (m-80) cc_final: 0.7570 (m-80) REVERT: A 703 ASN cc_start: 0.8206 (m110) cc_final: 0.7738 (m110) REVERT: A 718 LYS cc_start: 0.8244 (tppt) cc_final: 0.7943 (tptt) REVERT: A 729 GLU cc_start: 0.7943 (tp30) cc_final: 0.7647 (tp30) REVERT: A 734 ASN cc_start: 0.7991 (m-40) cc_final: 0.7645 (t0) REVERT: A 765 CYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7791 (t) REVERT: A 782 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6956 (t80) REVERT: A 783 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7985 (mmpt) REVERT: A 818 MET cc_start: 0.7335 (ppp) cc_final: 0.6643 (ppp) REVERT: A 819 LEU cc_start: 0.8089 (tp) cc_final: 0.6937 (mt) REVERT: A 855 MET cc_start: 0.6725 (mtm) cc_final: 0.6013 (mtm) REVERT: A 889 ARG cc_start: 0.7728 (tmm160) cc_final: 0.6961 (tmm160) REVERT: C 129 MET cc_start: 0.6761 (ppp) cc_final: 0.6323 (ppp) REVERT: D 7 LYS cc_start: 0.7663 (mttm) cc_final: 0.7330 (mttp) outliers start: 32 outliers final: 27 residues processed: 235 average time/residue: 0.2107 time to fit residues: 68.0804 Evaluate side-chains 253 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 8 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 0.0170 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9093 Z= 0.144 Angle : 0.573 11.042 12497 Z= 0.291 Chirality : 0.040 0.210 1426 Planarity : 0.004 0.053 1466 Dihedral : 11.293 115.316 1567 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.81 % Allowed : 22.33 % Favored : 74.86 % 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: -1.35 (0.26), residues: 997 helix: 0.11 (0.26), residues: 426 sheet: -1.77 (0.54), residues: 69 loop : -1.67 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 29 HIS 0.002 0.000 HIS A 309 PHE 0.023 0.001 PHE A 283 TYR 0.013 0.001 TYR A 689 ARG 0.005 0.000 ARG A 631 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7751 (mttt) cc_final: 0.7195 (mttm) REVERT: A 124 MET cc_start: 0.7641 (tpt) cc_final: 0.7265 (tpt) REVERT: A 150 ASN cc_start: 0.7761 (m110) cc_final: 0.7467 (m110) REVERT: A 241 LEU cc_start: 0.8332 (tp) cc_final: 0.8130 (tp) REVERT: A 242 MET cc_start: 0.7206 (mtp) cc_final: 0.6727 (mtp) REVERT: A 365 ARG cc_start: 0.7402 (mtt90) cc_final: 0.7157 (mtt90) REVERT: A 380 MET cc_start: 0.6994 (mmm) cc_final: 0.4954 (tmm) REVERT: A 395 CYS cc_start: 0.7538 (m) cc_final: 0.7333 (m) REVERT: A 438 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8004 (mmtt) REVERT: A 454 ASP cc_start: 0.7733 (t0) cc_final: 0.7340 (t0) REVERT: A 463 MET cc_start: 0.6295 (ppp) cc_final: 0.5887 (ppp) REVERT: A 466 ILE cc_start: 0.7584 (tp) cc_final: 0.7057 (mm) REVERT: A 645 CYS cc_start: 0.8093 (m) cc_final: 0.6557 (t) REVERT: A 668 MET cc_start: 0.7709 (tmm) cc_final: 0.7123 (tmm) REVERT: A 689 TYR cc_start: 0.7793 (m-80) cc_final: 0.7541 (m-80) REVERT: A 703 ASN cc_start: 0.8118 (m110) cc_final: 0.7663 (m110) REVERT: A 718 LYS cc_start: 0.8091 (tppt) cc_final: 0.7835 (tptt) REVERT: A 729 GLU cc_start: 0.7921 (tp30) cc_final: 0.7633 (tp30) REVERT: A 734 ASN cc_start: 0.7957 (m-40) cc_final: 0.7623 (t0) REVERT: A 765 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7672 (t) REVERT: A 782 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6836 (t80) REVERT: A 783 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7927 (mmpt) REVERT: A 818 MET cc_start: 0.7329 (ppp) cc_final: 0.6595 (ppp) REVERT: A 855 MET cc_start: 0.6676 (mtm) cc_final: 0.5978 (mtm) REVERT: A 881 PHE cc_start: 0.7567 (t80) cc_final: 0.7290 (t80) REVERT: A 889 ARG cc_start: 0.7658 (tmm160) cc_final: 0.6938 (tmm160) REVERT: C 129 MET cc_start: 0.6688 (ppp) cc_final: 0.6342 (ppp) REVERT: D 7 LYS cc_start: 0.7501 (mttm) cc_final: 0.7173 (mttp) outliers start: 25 outliers final: 20 residues processed: 240 average time/residue: 0.2102 time to fit residues: 69.1371 Evaluate side-chains 246 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 642 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138936 restraints weight = 15169.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143104 restraints weight = 8433.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145866 restraints weight = 5421.242| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9093 Z= 0.168 Angle : 0.581 10.198 12497 Z= 0.299 Chirality : 0.041 0.208 1426 Planarity : 0.004 0.056 1466 Dihedral : 11.289 116.305 1567 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.03 % Allowed : 22.22 % Favored : 74.75 % 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: -1.28 (0.26), residues: 997 helix: 0.18 (0.26), residues: 420 sheet: -1.73 (0.54), residues: 69 loop : -1.61 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 29 HIS 0.003 0.001 HIS A 133 PHE 0.025 0.001 PHE A 283 TYR 0.014 0.001 TYR A 689 ARG 0.006 0.000 ARG A 183 =============================================================================== Job complete usr+sys time: 1969.58 seconds wall clock time: 36 minutes 33.38 seconds (2193.38 seconds total)