Starting phenix.real_space_refine on Tue Aug 6 10:06:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcc_37099/08_2024/8kcc_37099.cif" } resolution = 3.1 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= -0.003 sd= 0.055 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: 7 Type Number sf(0) Gaussians P 302 5.49 5 S 34 5.16 5 Be 1 3.05 5 C 9342 2.51 5 N 2986 2.21 5 O 3603 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 65": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "H ARG 17": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "K GLU 334": "OE1" <-> "OE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 410": "OE1" <-> "OE2" Residue "K GLU 445": "OE1" <-> "OE2" Residue "K GLU 530": "OE1" <-> "OE2" Residue "K GLU 562": "OE1" <-> "OE2" Residue "K GLU 566": "OE1" <-> "OE2" Residue "K ARG 636": "NH1" <-> "NH2" Residue "K GLU 655": "OE1" <-> "OE2" Residue "K ARG 720": "NH1" <-> "NH2" Residue "K GLU 749": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16271 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "C" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 719 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3053 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3097 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4088 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 487} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.20, per 1000 atoms: 0.57 Number of scatterers: 16271 At special positions: 0 Unit cell: (134.734, 100.05, 142.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 P 302 15.00 F 3 9.00 O 3603 8.00 N 2986 7.00 C 9342 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 65.4% alpha, 6.9% beta 60 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.557A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.416A pdb=" N VAL A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.689A pdb=" N ILE B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 104 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 75 through 104 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 144 Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.528A pdb=" N ILE G 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.732A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 48 through 76 removed outlier: 4.479A pdb=" N GLU H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 232 through 247 removed outlier: 3.885A pdb=" N GLN K 236 " --> pdb=" O GLY K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 272 removed outlier: 4.188A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'K' and resid 310 through 318 Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.591A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 380 removed outlier: 3.932A pdb=" N SER K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 375 " --> pdb=" O GLU K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 394 removed outlier: 3.739A pdb=" N PHE K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 424 Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 489 through 498 Processing helix chain 'K' and resid 499 through 509 removed outlier: 3.905A pdb=" N LEU K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 removed outlier: 4.401A pdb=" N CYS K 523 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 540 Processing helix chain 'K' and resid 549 through 564 removed outlier: 3.599A pdb=" N LEU K 553 " --> pdb=" O TRP K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 623 through 632 removed outlier: 3.749A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 671 removed outlier: 4.001A pdb=" N LEU K 668 " --> pdb=" O SER K 664 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 669 " --> pdb=" O LYS K 665 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 removed outlier: 3.595A pdb=" N THR K 711 " --> pdb=" O LYS K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 723 removed outlier: 3.791A pdb=" N ASP K 723 " --> pdb=" O ASP K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.970A pdb=" N ARG A 51 " --> pdb=" O ILE D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 7.245A pdb=" N ARG B 51 " --> pdb=" O ILE C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.934A pdb=" N THR B 110 " --> pdb=" O TYR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.144A pdb=" N ARG E 83 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'F' and resid 83 through 84 removed outlier: 7.331A pdb=" N ARG F 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'K' and resid 224 through 225 removed outlier: 7.153A pdb=" N ILE K 224 " --> pdb=" O LEU K 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N TRP K 327 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.036A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER K 599 " --> pdb=" O CYS K 568 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE K 570 " --> pdb=" O SER K 599 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL K 543 " --> pdb=" O PHE K 596 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2974 1.33 - 1.45: 5348 1.45 - 1.57: 8200 1.57 - 1.69: 602 1.69 - 1.82: 57 Bond restraints: 17181 Sorted by residual: bond pdb=" C1' ADP K 801 " pdb=" C2' ADP K 801 " ideal model delta sigma weight residual 1.524 1.307 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.628 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C4' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.277 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C4 ADP K 801 " pdb=" C5 ADP K 801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" F2 BEF K 802 " pdb="BE BEF K 802 " ideal model delta sigma weight residual 1.476 1.366 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 17176 not shown) Histogram of bond angle deviations from ideal: 96.75 - 104.23: 1154 104.23 - 111.70: 9153 111.70 - 119.18: 5242 119.18 - 126.65: 7943 126.65 - 134.13: 985 Bond angle restraints: 24477 Sorted by residual: angle pdb=" N ARG H 17 " pdb=" CA ARG H 17 " pdb=" C ARG H 17 " ideal model delta sigma weight residual 109.52 96.75 12.77 1.55e+00 4.16e-01 6.79e+01 angle pdb=" N HIS H 18 " pdb=" CA HIS H 18 " pdb=" C HIS H 18 " ideal model delta sigma weight residual 110.24 99.80 10.44 1.47e+00 4.63e-01 5.05e+01 angle pdb=" N ARG H 19 " pdb=" CA ARG H 19 " pdb=" C ARG H 19 " ideal model delta sigma weight residual 109.85 119.37 -9.52 1.58e+00 4.01e-01 3.63e+01 angle pdb=" CA GLU D 91 " pdb=" CB GLU D 91 " pdb=" CG GLU D 91 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 ... (remaining 24472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.24: 7879 30.24 - 60.49: 1632 60.49 - 90.73: 56 90.73 - 120.98: 1 120.98 - 151.22: 3 Dihedral angle restraints: 9571 sinusoidal: 5912 harmonic: 3659 Sorted by residual: dihedral pdb=" C4' ADP K 801 " pdb=" C5' ADP K 801 " pdb=" O5' ADP K 801 " pdb=" PA ADP K 801 " ideal model delta sinusoidal sigma weight residual 180.00 77.08 102.92 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" CA GLN K 366 " pdb=" C GLN K 366 " pdb=" N ASN K 367 " pdb=" CA ASN K 367 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 68.78 151.22 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2424 0.046 - 0.092: 279 0.092 - 0.139: 67 0.139 - 0.185: 2 0.185 - 0.231: 4 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ARG H 19 " pdb=" N ARG H 19 " pdb=" C ARG H 19 " pdb=" CB ARG H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG H 17 " pdb=" N ARG H 17 " pdb=" C ARG H 17 " pdb=" CB ARG H 17 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASP H 24 " pdb=" N ASP H 24 " pdb=" C ASP H 24 " pdb=" CB ASP H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2773 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 652 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" CD GLN K 652 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN K 652 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN K 652 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.021 2.00e-02 2.50e+03 9.24e-03 2.56e+00 pdb=" N9 DG I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 94 " -0.017 2.00e-02 2.50e+03 8.97e-03 2.21e+00 pdb=" N9 DA I 94 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 94 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 94 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 94 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 94 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 94 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1295 2.74 - 3.28: 15815 3.28 - 3.82: 31079 3.82 - 4.36: 35745 4.36 - 4.90: 53697 Nonbonded interactions: 137631 Sorted by model distance: nonbonded pdb=" OG SER K 386 " pdb=" OD1 ASP K 388 " model vdw 2.199 3.040 nonbonded pdb=" O LEU C 93 " pdb=" OG SER C 97 " model vdw 2.218 3.040 nonbonded pdb=" O LEU D 93 " pdb=" OG SER D 97 " model vdw 2.219 3.040 nonbonded pdb=" O2 DT I 60 " pdb=" N2 DG J 92 " model vdw 2.221 3.120 nonbonded pdb=" O2 DT I 49 " pdb=" N2 DG J 103 " model vdw 2.225 3.120 ... (remaining 137626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 24 through 125) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 23 through 102) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 50.640 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 17181 Z= 0.272 Angle : 0.550 12.768 24477 Z= 0.323 Chirality : 0.033 0.231 2776 Planarity : 0.003 0.032 2050 Dihedral : 25.142 151.222 7207 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.20 % Allowed : 1.75 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1244 helix: 0.77 (0.17), residues: 798 sheet: -1.70 (0.56), residues: 66 loop : -1.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 212 HIS 0.010 0.001 HIS K 670 PHE 0.012 0.001 PHE K 459 TYR 0.008 0.001 TYR B 66 ARG 0.003 0.000 ARG H 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 279 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9468 (tttt) cc_final: 0.8939 (tttm) REVERT: A 70 GLU cc_start: 0.8277 (tp30) cc_final: 0.7851 (tp30) REVERT: A 84 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7770 (mmmt) REVERT: A 99 ASP cc_start: 0.8687 (t70) cc_final: 0.8168 (t0) REVERT: A 101 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 26 LYS cc_start: 0.9205 (mttt) cc_final: 0.8962 (mtmm) REVERT: B 47 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8229 (mtp180) REVERT: B 70 GLU cc_start: 0.8309 (tp30) cc_final: 0.7896 (tp30) REVERT: B 73 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7875 (tp30) REVERT: B 81 ASP cc_start: 0.8988 (m-30) cc_final: 0.8756 (m-30) REVERT: B 99 ASP cc_start: 0.8610 (t0) cc_final: 0.8200 (t0) REVERT: C 52 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (tppt) REVERT: C 71 ASP cc_start: 0.8704 (p0) cc_final: 0.8341 (p0) REVERT: C 88 ASP cc_start: 0.8141 (t0) cc_final: 0.7867 (t0) REVERT: C 113 GLU cc_start: 0.8409 (mp0) cc_final: 0.8092 (mp0) REVERT: D 79 MET cc_start: 0.8647 (tpp) cc_final: 0.8363 (tpp) REVERT: D 84 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9357 (m) REVERT: D 88 ASP cc_start: 0.8536 (t0) cc_final: 0.8011 (t0) REVERT: D 96 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 113 GLU cc_start: 0.8135 (mp0) cc_final: 0.7753 (mp0) REVERT: F 50 GLU cc_start: 0.8957 (tt0) cc_final: 0.8652 (tt0) REVERT: F 125 GLN cc_start: 0.9172 (mt0) cc_final: 0.8957 (mt0) REVERT: G 59 LYS cc_start: 0.8429 (tttt) cc_final: 0.8194 (tttm) REVERT: G 100 PHE cc_start: 0.8254 (m-80) cc_final: 0.7840 (m-80) REVERT: H 26 ILE cc_start: 0.9300 (tp) cc_final: 0.9070 (tp) REVERT: H 59 LYS cc_start: 0.8829 (tttt) cc_final: 0.8546 (tttp) REVERT: H 79 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8603 (mmtm) REVERT: H 98 TYR cc_start: 0.8434 (m-10) cc_final: 0.8169 (m-10) REVERT: K 284 ASP cc_start: 0.8369 (t70) cc_final: 0.8100 (t0) REVERT: K 296 MET cc_start: 0.8463 (ppp) cc_final: 0.8089 (ppp) REVERT: K 354 MET cc_start: 0.8710 (pmm) cc_final: 0.8320 (pmm) REVERT: K 452 MET cc_start: 0.7928 (ttp) cc_final: 0.7394 (ttm) REVERT: K 556 MET cc_start: 0.9437 (mtm) cc_final: 0.8582 (ptm) REVERT: K 631 MET cc_start: 0.9234 (ptm) cc_final: 0.8820 (ptp) REVERT: K 758 MET cc_start: 0.5691 (tpt) cc_final: 0.5036 (tpp) outliers start: 13 outliers final: 3 residues processed: 288 average time/residue: 0.3326 time to fit residues: 134.0582 Evaluate side-chains 205 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain H residue 17 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN C 69 HIS D 69 HIS D 115 GLN E 39 HIS E 68 GLN E 113 HIS F 85 GLN F 93 GLN H 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS K 336 HIS ** K 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 639 GLN K 644 HIS K 710 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17181 Z= 0.440 Angle : 0.705 10.571 24477 Z= 0.392 Chirality : 0.043 0.200 2776 Planarity : 0.005 0.053 2050 Dihedral : 29.550 151.905 4685 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.77 % Allowed : 12.36 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1244 helix: 1.90 (0.18), residues: 803 sheet: -1.38 (0.57), residues: 68 loop : -0.97 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 748 HIS 0.012 0.002 HIS H 18 PHE 0.038 0.002 PHE F 41 TYR 0.017 0.002 TYR K 513 ARG 0.006 0.001 ARG K 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9177 (mttp) cc_final: 0.8782 (mttp) REVERT: A 44 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8969 (mtpt) REVERT: A 70 GLU cc_start: 0.8423 (tp30) cc_final: 0.8043 (tp30) REVERT: A 81 ASP cc_start: 0.8677 (m-30) cc_final: 0.8472 (t0) REVERT: A 101 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 73 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7870 (tp30) REVERT: B 81 ASP cc_start: 0.9002 (m-30) cc_final: 0.8784 (m-30) REVERT: B 99 ASP cc_start: 0.8693 (t0) cc_final: 0.8379 (t0) REVERT: B 101 GLU cc_start: 0.8001 (pm20) cc_final: 0.7627 (pm20) REVERT: C 82 MET cc_start: 0.9297 (mmm) cc_final: 0.8866 (tpp) REVERT: C 88 ASP cc_start: 0.8630 (t0) cc_final: 0.8338 (t0) REVERT: C 91 GLU cc_start: 0.8298 (tt0) cc_final: 0.8057 (tp30) REVERT: C 96 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7932 (mm-30) REVERT: D 88 ASP cc_start: 0.8735 (t0) cc_final: 0.8101 (t0) REVERT: D 91 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 113 GLU cc_start: 0.8465 (mp0) cc_final: 0.7535 (mp0) REVERT: E 50 GLU cc_start: 0.8606 (tt0) cc_final: 0.8006 (tt0) REVERT: E 115 LYS cc_start: 0.9207 (mttm) cc_final: 0.8992 (mmtt) REVERT: F 53 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8822 (ttpp) REVERT: G 59 LYS cc_start: 0.8661 (tttt) cc_final: 0.8268 (tttm) REVERT: G 100 PHE cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-80) REVERT: H 27 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8607 (mm-40) REVERT: H 79 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8619 (mmtp) REVERT: K 284 ASP cc_start: 0.8435 (t70) cc_final: 0.8118 (t70) REVERT: K 296 MET cc_start: 0.8666 (ppp) cc_final: 0.8376 (ppp) REVERT: K 354 MET cc_start: 0.8981 (pmm) cc_final: 0.8580 (pmm) REVERT: K 452 MET cc_start: 0.8027 (ttp) cc_final: 0.7512 (ttt) REVERT: K 454 ASP cc_start: 0.9198 (p0) cc_final: 0.8884 (t0) REVERT: K 502 LEU cc_start: 0.8532 (tp) cc_final: 0.8215 (tp) REVERT: K 556 MET cc_start: 0.9381 (mtm) cc_final: 0.8466 (ptp) REVERT: K 758 MET cc_start: 0.5606 (tpt) cc_final: 0.5041 (tpp) outliers start: 30 outliers final: 22 residues processed: 223 average time/residue: 0.3091 time to fit residues: 99.3877 Evaluate side-chains 203 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 343 CYS Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 39 HIS F 68 GLN F 113 HIS H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN K 336 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17181 Z= 0.227 Angle : 0.553 7.838 24477 Z= 0.315 Chirality : 0.035 0.153 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.286 154.825 4678 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 15.22 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1244 helix: 2.32 (0.18), residues: 804 sheet: -1.29 (0.56), residues: 68 loop : -0.83 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.007 0.001 HIS K 336 PHE 0.013 0.001 PHE E 41 TYR 0.012 0.001 TYR B 66 ARG 0.007 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9160 (mttp) cc_final: 0.8913 (mttp) REVERT: A 28 MET cc_start: 0.8898 (tmm) cc_final: 0.8480 (tmm) REVERT: A 70 GLU cc_start: 0.8419 (tp30) cc_final: 0.7964 (tp30) REVERT: A 73 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 99 ASP cc_start: 0.8557 (t0) cc_final: 0.8249 (t0) REVERT: B 41 ARG cc_start: 0.9349 (ttp-170) cc_final: 0.8967 (ttp80) REVERT: B 48 TYR cc_start: 0.9481 (m-80) cc_final: 0.9190 (m-80) REVERT: B 99 ASP cc_start: 0.8665 (t0) cc_final: 0.8319 (t0) REVERT: B 101 GLU cc_start: 0.7861 (pm20) cc_final: 0.7391 (pm20) REVERT: C 88 ASP cc_start: 0.8583 (t0) cc_final: 0.8279 (t0) REVERT: C 96 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 113 GLU cc_start: 0.8353 (mp0) cc_final: 0.7502 (mp0) REVERT: D 55 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7018 (mm-30) REVERT: D 57 TYR cc_start: 0.9306 (m-80) cc_final: 0.9031 (m-80) REVERT: D 88 ASP cc_start: 0.8711 (t0) cc_final: 0.8062 (t0) REVERT: D 91 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 113 GLU cc_start: 0.8394 (mp0) cc_final: 0.7469 (mp0) REVERT: E 50 GLU cc_start: 0.8616 (tt0) cc_final: 0.7944 (tt0) REVERT: E 115 LYS cc_start: 0.9156 (mttm) cc_final: 0.8898 (mmtm) REVERT: F 50 GLU cc_start: 0.9102 (tt0) cc_final: 0.8798 (tt0) REVERT: G 59 LYS cc_start: 0.8569 (tttt) cc_final: 0.8216 (tttm) REVERT: G 100 PHE cc_start: 0.8732 (m-80) cc_final: 0.8457 (m-80) REVERT: H 16 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8393 (mmtm) REVERT: H 27 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8599 (mm-40) REVERT: H 79 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8597 (mmtp) REVERT: K 296 MET cc_start: 0.8843 (ppp) cc_final: 0.8540 (ppp) REVERT: K 344 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8664 (mmtp) REVERT: K 354 MET cc_start: 0.8753 (pmm) cc_final: 0.8444 (pmm) REVERT: K 373 TRP cc_start: 0.9149 (t60) cc_final: 0.8835 (t60) REVERT: K 452 MET cc_start: 0.7935 (ttp) cc_final: 0.7337 (ttt) REVERT: K 556 MET cc_start: 0.9343 (mtm) cc_final: 0.8429 (ptp) REVERT: K 758 MET cc_start: 0.5517 (tpt) cc_final: 0.5075 (mmm) outliers start: 16 outliers final: 12 residues processed: 209 average time/residue: 0.2891 time to fit residues: 88.4606 Evaluate side-chains 198 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 147 optimal weight: 0.0870 chunk 132 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS F 68 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17181 Z= 0.303 Angle : 0.577 8.163 24477 Z= 0.328 Chirality : 0.036 0.139 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.361 158.265 4678 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.75 % Allowed : 16.42 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.24), residues: 1244 helix: 2.51 (0.18), residues: 804 sheet: -1.43 (0.53), residues: 78 loop : -0.75 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.026 0.001 HIS K 499 PHE 0.014 0.001 PHE F 78 TYR 0.012 0.001 TYR B 66 ARG 0.007 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9194 (mttp) cc_final: 0.8943 (mttp) REVERT: A 70 GLU cc_start: 0.8459 (tp30) cc_final: 0.8018 (tp30) REVERT: A 73 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 83 LYS cc_start: 0.9292 (mptt) cc_final: 0.9061 (mppt) REVERT: A 99 ASP cc_start: 0.8812 (t0) cc_final: 0.8238 (t0) REVERT: B 41 ARG cc_start: 0.9338 (ttp-170) cc_final: 0.8851 (ttp80) REVERT: B 48 TYR cc_start: 0.9317 (m-80) cc_final: 0.8980 (m-80) REVERT: B 73 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: B 99 ASP cc_start: 0.8744 (t0) cc_final: 0.8314 (t0) REVERT: B 101 GLU cc_start: 0.7962 (pm20) cc_final: 0.7666 (pm20) REVERT: C 88 ASP cc_start: 0.8584 (t0) cc_final: 0.8296 (t0) REVERT: C 91 GLU cc_start: 0.8763 (tp30) cc_final: 0.8205 (tp30) REVERT: C 96 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7941 (mm-30) REVERT: C 113 GLU cc_start: 0.8394 (mp0) cc_final: 0.7460 (mp0) REVERT: D 57 TYR cc_start: 0.9393 (m-80) cc_final: 0.9003 (m-80) REVERT: D 88 ASP cc_start: 0.8725 (t0) cc_final: 0.8083 (t0) REVERT: D 91 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7970 (tm-30) REVERT: E 50 GLU cc_start: 0.8598 (tt0) cc_final: 0.7933 (tt0) REVERT: E 54 TYR cc_start: 0.8983 (m-80) cc_final: 0.8651 (m-80) REVERT: E 115 LYS cc_start: 0.9194 (mttm) cc_final: 0.8953 (mmtt) REVERT: E 134 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7489 (mmm160) REVERT: F 50 GLU cc_start: 0.9165 (tt0) cc_final: 0.8925 (tt0) REVERT: G 59 LYS cc_start: 0.8606 (tttt) cc_final: 0.8253 (tttm) REVERT: G 100 PHE cc_start: 0.8859 (m-80) cc_final: 0.8558 (m-80) REVERT: H 16 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8305 (mmtm) REVERT: H 27 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8778 (mm-40) REVERT: H 79 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8651 (mmtp) REVERT: K 296 MET cc_start: 0.8850 (ppp) cc_final: 0.8529 (ppp) REVERT: K 354 MET cc_start: 0.8680 (pmm) cc_final: 0.8252 (pmm) REVERT: K 373 TRP cc_start: 0.9171 (t60) cc_final: 0.8835 (t60) REVERT: K 452 MET cc_start: 0.7918 (ttp) cc_final: 0.7513 (ttt) REVERT: K 499 HIS cc_start: 0.6104 (p-80) cc_final: 0.5776 (p-80) REVERT: K 502 LEU cc_start: 0.8394 (tp) cc_final: 0.8042 (tp) REVERT: K 552 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9163 (mt) REVERT: K 758 MET cc_start: 0.5512 (tpt) cc_final: 0.5070 (mmm) outliers start: 19 outliers final: 13 residues processed: 196 average time/residue: 0.2916 time to fit residues: 84.2137 Evaluate side-chains 193 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 552 LEU Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS F 68 GLN G 93 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17181 Z= 0.288 Angle : 0.573 8.912 24477 Z= 0.325 Chirality : 0.036 0.134 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.434 161.419 4678 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 17.71 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1244 helix: 2.53 (0.18), residues: 810 sheet: -1.42 (0.53), residues: 78 loop : -0.70 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.017 0.001 HIS K 499 PHE 0.015 0.001 PHE F 78 TYR 0.013 0.001 TYR B 66 ARG 0.006 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9153 (mttp) cc_final: 0.8707 (mttp) REVERT: A 47 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8043 (ptm160) REVERT: A 70 GLU cc_start: 0.8442 (tp30) cc_final: 0.7997 (tp30) REVERT: A 73 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 99 ASP cc_start: 0.8759 (t0) cc_final: 0.8176 (t0) REVERT: B 41 ARG cc_start: 0.9323 (ttp-170) cc_final: 0.8854 (ttp80) REVERT: B 48 TYR cc_start: 0.9144 (m-80) cc_final: 0.8629 (m-80) REVERT: B 73 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: B 99 ASP cc_start: 0.8712 (t0) cc_final: 0.8249 (t0) REVERT: B 101 GLU cc_start: 0.8025 (pm20) cc_final: 0.7673 (pm20) REVERT: C 88 ASP cc_start: 0.8572 (t0) cc_final: 0.8292 (t0) REVERT: C 91 GLU cc_start: 0.8815 (tp30) cc_final: 0.8386 (tp30) REVERT: C 96 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 113 GLU cc_start: 0.8404 (mp0) cc_final: 0.7461 (mp0) REVERT: D 57 TYR cc_start: 0.9373 (m-80) cc_final: 0.9026 (m-80) REVERT: D 88 ASP cc_start: 0.8722 (t0) cc_final: 0.8211 (t0) REVERT: D 91 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 113 GLU cc_start: 0.8511 (mp0) cc_final: 0.7793 (mp0) REVERT: E 50 GLU cc_start: 0.8663 (tt0) cc_final: 0.7974 (tt0) REVERT: E 54 TYR cc_start: 0.8914 (m-80) cc_final: 0.8530 (m-80) REVERT: E 115 LYS cc_start: 0.9194 (mttm) cc_final: 0.8937 (mptt) REVERT: E 134 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7501 (mmm160) REVERT: F 50 GLU cc_start: 0.9171 (tt0) cc_final: 0.8897 (tt0) REVERT: G 53 GLU cc_start: 0.8629 (tp30) cc_final: 0.8206 (tp30) REVERT: G 59 LYS cc_start: 0.8631 (tttt) cc_final: 0.8307 (tttm) REVERT: H 79 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8731 (mmtm) REVERT: H 98 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8045 (m-10) REVERT: K 296 MET cc_start: 0.8919 (ppp) cc_final: 0.8208 (ppp) REVERT: K 354 MET cc_start: 0.8682 (pmm) cc_final: 0.8106 (pmm) REVERT: K 452 MET cc_start: 0.8028 (ttp) cc_final: 0.7688 (ttt) REVERT: K 502 LEU cc_start: 0.8386 (tp) cc_final: 0.7810 (tp) REVERT: K 758 MET cc_start: 0.5500 (tpt) cc_final: 0.5049 (mmm) outliers start: 20 outliers final: 14 residues processed: 202 average time/residue: 0.3020 time to fit residues: 89.4801 Evaluate side-chains 195 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN E 68 GLN F 39 HIS F 68 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN K 541 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17181 Z= 0.405 Angle : 0.634 8.731 24477 Z= 0.357 Chirality : 0.039 0.147 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.852 167.369 4678 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.31 % Allowed : 18.17 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1244 helix: 2.46 (0.18), residues: 813 sheet: -1.50 (0.54), residues: 78 loop : -0.72 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 373 HIS 0.008 0.001 HIS C 129 PHE 0.017 0.002 PHE F 78 TYR 0.014 0.002 TYR C 57 ARG 0.014 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9155 (mttp) cc_final: 0.8738 (mttp) REVERT: A 28 MET cc_start: 0.8947 (tmm) cc_final: 0.8521 (tmm) REVERT: A 70 GLU cc_start: 0.8497 (tp30) cc_final: 0.8046 (tp30) REVERT: A 73 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 99 ASP cc_start: 0.8762 (t0) cc_final: 0.8103 (t0) REVERT: B 41 ARG cc_start: 0.9340 (ttp-170) cc_final: 0.8814 (ttp80) REVERT: B 50 GLN cc_start: 0.8998 (tp40) cc_final: 0.8166 (mm-40) REVERT: B 73 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: B 99 ASP cc_start: 0.8726 (t0) cc_final: 0.7984 (t0) REVERT: B 101 GLU cc_start: 0.7903 (pm20) cc_final: 0.7700 (pm20) REVERT: C 88 ASP cc_start: 0.8629 (t0) cc_final: 0.8333 (t0) REVERT: C 96 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 113 GLU cc_start: 0.8448 (mp0) cc_final: 0.7481 (mp0) REVERT: C 129 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8507 (m-70) REVERT: D 88 ASP cc_start: 0.8730 (t0) cc_final: 0.8193 (t0) REVERT: D 91 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 113 GLU cc_start: 0.8417 (mp0) cc_final: 0.8095 (mp0) REVERT: E 50 GLU cc_start: 0.8660 (tt0) cc_final: 0.7954 (tt0) REVERT: E 54 TYR cc_start: 0.9063 (m-80) cc_final: 0.8621 (m-80) REVERT: E 115 LYS cc_start: 0.9233 (mttm) cc_final: 0.9006 (mmtt) REVERT: E 120 MET cc_start: 0.8587 (mtp) cc_final: 0.8011 (mtp) REVERT: E 134 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7517 (mmm160) REVERT: F 50 GLU cc_start: 0.9162 (tt0) cc_final: 0.8887 (tt0) REVERT: G 53 GLU cc_start: 0.8609 (tp30) cc_final: 0.8350 (tp30) REVERT: G 59 LYS cc_start: 0.8648 (tttt) cc_final: 0.8293 (tttm) REVERT: H 44 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8041 (mtpt) REVERT: H 79 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8763 (mmtm) REVERT: H 98 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: K 296 MET cc_start: 0.8883 (ppp) cc_final: 0.8676 (ppp) REVERT: K 354 MET cc_start: 0.8724 (pmm) cc_final: 0.8136 (pmm) REVERT: K 626 MET cc_start: 0.8892 (tpp) cc_final: 0.8631 (tpp) REVERT: K 758 MET cc_start: 0.5818 (tpt) cc_final: 0.5418 (mmm) outliers start: 25 outliers final: 19 residues processed: 196 average time/residue: 0.2958 time to fit residues: 84.3720 Evaluate side-chains 195 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS E 68 GLN F 39 HIS F 68 GLN G 93 GLN H 18 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 456 GLN ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17181 Z= 0.214 Angle : 0.563 11.305 24477 Z= 0.319 Chirality : 0.034 0.135 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.586 171.477 4678 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.57 % Allowed : 19.37 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.24), residues: 1244 helix: 2.65 (0.18), residues: 810 sheet: -1.39 (0.53), residues: 78 loop : -0.62 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.009 0.001 HIS C 129 PHE 0.010 0.001 PHE F 78 TYR 0.012 0.001 TYR B 66 ARG 0.008 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9141 (mttp) cc_final: 0.8708 (mttp) REVERT: A 70 GLU cc_start: 0.8431 (tp30) cc_final: 0.7960 (tp30) REVERT: A 99 ASP cc_start: 0.8783 (t0) cc_final: 0.8085 (t0) REVERT: B 41 ARG cc_start: 0.9263 (ttp-170) cc_final: 0.8835 (ttp80) REVERT: B 50 GLN cc_start: 0.8789 (tp40) cc_final: 0.8542 (mm-40) REVERT: B 73 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: B 99 ASP cc_start: 0.8697 (t0) cc_final: 0.7879 (t0) REVERT: C 88 ASP cc_start: 0.8560 (t0) cc_final: 0.8279 (t0) REVERT: C 96 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 113 GLU cc_start: 0.8469 (mp0) cc_final: 0.7531 (mp0) REVERT: D 57 TYR cc_start: 0.9341 (m-80) cc_final: 0.9069 (m-80) REVERT: D 88 ASP cc_start: 0.8717 (t0) cc_final: 0.8059 (t0) REVERT: D 91 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 113 GLU cc_start: 0.8423 (mp0) cc_final: 0.8132 (mp0) REVERT: E 50 GLU cc_start: 0.8667 (tt0) cc_final: 0.7976 (tt0) REVERT: E 54 TYR cc_start: 0.8957 (m-80) cc_final: 0.8612 (m-80) REVERT: E 115 LYS cc_start: 0.9229 (mttm) cc_final: 0.8961 (mptt) REVERT: E 134 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7695 (mmm160) REVERT: F 50 GLU cc_start: 0.9183 (tt0) cc_final: 0.8879 (tt0) REVERT: G 53 GLU cc_start: 0.8537 (tp30) cc_final: 0.8175 (tp30) REVERT: G 59 LYS cc_start: 0.8607 (tttt) cc_final: 0.8288 (tttm) REVERT: H 79 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8783 (mmtm) REVERT: K 296 MET cc_start: 0.8894 (ppp) cc_final: 0.8187 (ppp) REVERT: K 354 MET cc_start: 0.8640 (pmm) cc_final: 0.8044 (pmm) REVERT: K 373 TRP cc_start: 0.9099 (t60) cc_final: 0.8757 (t60) REVERT: K 502 LEU cc_start: 0.7825 (tp) cc_final: 0.7577 (tp) REVERT: K 758 MET cc_start: 0.5730 (tpt) cc_final: 0.5324 (mmm) outliers start: 17 outliers final: 14 residues processed: 200 average time/residue: 0.3109 time to fit residues: 91.9654 Evaluate side-chains 197 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 608 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17181 Z= 0.222 Angle : 0.565 10.277 24477 Z= 0.319 Chirality : 0.034 0.131 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.509 175.842 4678 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.24), residues: 1244 helix: 2.67 (0.18), residues: 810 sheet: -1.37 (0.53), residues: 78 loop : -0.53 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.003 0.001 HIS D 129 PHE 0.013 0.001 PHE F 78 TYR 0.011 0.001 TYR A 48 ARG 0.005 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9190 (mttp) cc_final: 0.8723 (mttp) REVERT: A 38 ARG cc_start: 0.8640 (ttm170) cc_final: 0.8434 (ttm170) REVERT: A 70 GLU cc_start: 0.8457 (tp30) cc_final: 0.8004 (tp30) REVERT: A 99 ASP cc_start: 0.8781 (t0) cc_final: 0.8096 (t0) REVERT: B 41 ARG cc_start: 0.9328 (ttp-170) cc_final: 0.8858 (ttp80) REVERT: B 50 GLN cc_start: 0.8777 (tp40) cc_final: 0.8443 (mm-40) REVERT: B 73 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: B 99 ASP cc_start: 0.8661 (t0) cc_final: 0.8093 (t0) REVERT: C 88 ASP cc_start: 0.8568 (t0) cc_final: 0.8292 (t0) REVERT: C 96 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7930 (mm-30) REVERT: C 113 GLU cc_start: 0.8504 (mp0) cc_final: 0.7538 (mp0) REVERT: D 57 TYR cc_start: 0.9330 (m-80) cc_final: 0.9080 (m-80) REVERT: D 88 ASP cc_start: 0.8722 (t0) cc_final: 0.8064 (t0) REVERT: D 91 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8013 (tm-30) REVERT: D 113 GLU cc_start: 0.8384 (mp0) cc_final: 0.8166 (mp0) REVERT: E 50 GLU cc_start: 0.8726 (tt0) cc_final: 0.8011 (tt0) REVERT: E 54 TYR cc_start: 0.8930 (m-80) cc_final: 0.8568 (m-80) REVERT: E 115 LYS cc_start: 0.9222 (mttm) cc_final: 0.8969 (mptt) REVERT: E 134 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7692 (mmm160) REVERT: F 50 GLU cc_start: 0.9150 (tt0) cc_final: 0.8837 (tt0) REVERT: F 53 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8893 (ttpp) REVERT: G 53 GLU cc_start: 0.8513 (tp30) cc_final: 0.8307 (tp30) REVERT: G 59 LYS cc_start: 0.8603 (tttt) cc_final: 0.8312 (tttm) REVERT: H 79 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8736 (mmtm) REVERT: K 296 MET cc_start: 0.8880 (ppp) cc_final: 0.8279 (ppp) REVERT: K 354 MET cc_start: 0.8653 (pmm) cc_final: 0.8022 (pmm) REVERT: K 373 TRP cc_start: 0.9152 (t60) cc_final: 0.8823 (t60) REVERT: K 758 MET cc_start: 0.5748 (tpt) cc_final: 0.5336 (mmm) outliers start: 22 outliers final: 15 residues processed: 203 average time/residue: 0.2886 time to fit residues: 85.9987 Evaluate side-chains 200 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 30.0000 chunk 129 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17181 Z= 0.332 Angle : 0.619 12.033 24477 Z= 0.345 Chirality : 0.037 0.163 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.761 176.495 4678 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 19.74 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1244 helix: 2.62 (0.18), residues: 810 sheet: -1.47 (0.52), residues: 78 loop : -0.55 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.005 0.001 HIS D 129 PHE 0.015 0.001 PHE F 78 TYR 0.010 0.001 TYR D 57 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9190 (mttp) cc_final: 0.8755 (mttp) REVERT: A 38 ARG cc_start: 0.8618 (ttm170) cc_final: 0.8365 (ttm170) REVERT: A 47 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8347 (ttp-170) REVERT: A 70 GLU cc_start: 0.8437 (tp30) cc_final: 0.7978 (tp30) REVERT: A 83 LYS cc_start: 0.9091 (mppt) cc_final: 0.8715 (mppt) REVERT: A 99 ASP cc_start: 0.8804 (t0) cc_final: 0.8138 (t0) REVERT: B 41 ARG cc_start: 0.9374 (ttp-170) cc_final: 0.8882 (ttp80) REVERT: B 73 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: B 99 ASP cc_start: 0.8648 (t0) cc_final: 0.8143 (t0) REVERT: C 88 ASP cc_start: 0.8594 (t0) cc_final: 0.8320 (t0) REVERT: C 96 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8023 (mm-30) REVERT: C 113 GLU cc_start: 0.8440 (mp0) cc_final: 0.7479 (mp0) REVERT: D 88 ASP cc_start: 0.8738 (t0) cc_final: 0.8103 (t0) REVERT: D 91 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 113 GLU cc_start: 0.8429 (mp0) cc_final: 0.8138 (mp0) REVERT: E 50 GLU cc_start: 0.8716 (tt0) cc_final: 0.7995 (tt0) REVERT: E 54 TYR cc_start: 0.8980 (m-80) cc_final: 0.8579 (m-80) REVERT: E 115 LYS cc_start: 0.9267 (mttm) cc_final: 0.9028 (mmtt) REVERT: F 50 GLU cc_start: 0.9165 (tt0) cc_final: 0.8836 (tt0) REVERT: F 53 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8883 (ttpp) REVERT: G 53 GLU cc_start: 0.8621 (tp30) cc_final: 0.8252 (tp30) REVERT: G 59 LYS cc_start: 0.8623 (tttt) cc_final: 0.8284 (tttm) REVERT: H 79 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8764 (mmtm) REVERT: K 296 MET cc_start: 0.8866 (ppp) cc_final: 0.8259 (ppp) REVERT: K 354 MET cc_start: 0.8719 (pmm) cc_final: 0.8046 (pmm) REVERT: K 373 TRP cc_start: 0.9148 (t60) cc_final: 0.8782 (t60) REVERT: K 758 MET cc_start: 0.5867 (tpt) cc_final: 0.5402 (mmm) outliers start: 20 outliers final: 16 residues processed: 187 average time/residue: 0.2957 time to fit residues: 81.2430 Evaluate side-chains 190 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.0970 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 140 optimal weight: 0.0670 chunk 121 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17181 Z= 0.187 Angle : 0.575 10.648 24477 Z= 0.321 Chirality : 0.034 0.166 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.489 178.594 4678 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.38 % Allowed : 20.66 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.24), residues: 1244 helix: 2.63 (0.18), residues: 809 sheet: -1.33 (0.51), residues: 78 loop : -0.45 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.005 0.001 HIS D 129 PHE 0.011 0.001 PHE F 78 TYR 0.011 0.001 TYR C 57 ARG 0.004 0.000 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9168 (mttp) cc_final: 0.8704 (mttp) REVERT: A 38 ARG cc_start: 0.8570 (ttm170) cc_final: 0.8346 (ttm170) REVERT: A 70 GLU cc_start: 0.8388 (tp30) cc_final: 0.7939 (tp30) REVERT: A 83 LYS cc_start: 0.9125 (mppt) cc_final: 0.8879 (mppt) REVERT: A 99 ASP cc_start: 0.8809 (t0) cc_final: 0.8144 (t0) REVERT: B 41 ARG cc_start: 0.9229 (ttp-170) cc_final: 0.8844 (ttp80) REVERT: B 73 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: B 99 ASP cc_start: 0.8639 (t0) cc_final: 0.8064 (t0) REVERT: C 88 ASP cc_start: 0.8557 (t0) cc_final: 0.8282 (t0) REVERT: C 96 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7925 (mm-30) REVERT: C 113 GLU cc_start: 0.8481 (mp0) cc_final: 0.7510 (mp0) REVERT: C 129 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (m90) REVERT: D 53 ASN cc_start: 0.9133 (t0) cc_final: 0.8905 (t0) REVERT: D 88 ASP cc_start: 0.8698 (t0) cc_final: 0.8091 (t0) REVERT: D 91 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 50 GLU cc_start: 0.8739 (tt0) cc_final: 0.8030 (tt0) REVERT: E 54 TYR cc_start: 0.8914 (m-80) cc_final: 0.8574 (m-80) REVERT: E 115 LYS cc_start: 0.9204 (mttm) cc_final: 0.8945 (mptt) REVERT: F 50 GLU cc_start: 0.9144 (tt0) cc_final: 0.8821 (tt0) REVERT: F 94 GLU cc_start: 0.8484 (tp30) cc_final: 0.8213 (tt0) REVERT: G 59 LYS cc_start: 0.8574 (tttt) cc_final: 0.8285 (tttm) REVERT: G 84 MET cc_start: 0.8344 (tpp) cc_final: 0.7782 (mmm) REVERT: H 79 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8748 (mmtm) REVERT: K 296 MET cc_start: 0.8908 (ppp) cc_final: 0.8286 (ppp) REVERT: K 354 MET cc_start: 0.8655 (pmm) cc_final: 0.7988 (pmm) REVERT: K 373 TRP cc_start: 0.9140 (t60) cc_final: 0.8814 (t60) REVERT: K 758 MET cc_start: 0.5713 (tpt) cc_final: 0.5511 (tpp) outliers start: 15 outliers final: 12 residues processed: 200 average time/residue: 0.2822 time to fit residues: 83.3538 Evaluate side-chains 196 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 552 LEU Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.087223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056423 restraints weight = 56532.297| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.92 r_work: 0.2858 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17181 Z= 0.180 Angle : 0.569 10.522 24477 Z= 0.317 Chirality : 0.034 0.172 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.442 178.159 4678 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.11 % Allowed : 21.22 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.24), residues: 1244 helix: 2.69 (0.18), residues: 809 sheet: -1.31 (0.51), residues: 78 loop : -0.40 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.010 0.001 HIS D 129 PHE 0.011 0.001 PHE F 78 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.000 ARG K 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.98 seconds wall clock time: 59 minutes 11.96 seconds (3551.96 seconds total)