Starting phenix.real_space_refine on Wed Mar 4 15:35:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb9_21587/03_2026/6wb9_21587.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 9399 2.51 5 N 2319 2.21 5 O 2725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14507 Number of models: 1 Model: "" Number of chains: 12 Chain: "0" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 902 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5275 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 4 Chain: "2" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2377 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "3" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1591 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Chain: "4" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1197 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain breaks: 2 Chain: "5" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Chain: "6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 804 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "7" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1160 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain breaks: 2 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "5" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.29, per 1000 atoms: 0.23 Number of scatterers: 14507 At special positions: 0 Unit cell: (158.466, 142.002, 119.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2725 8.00 N 2319 7.00 C 9399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 0 65 " - pdb=" SG CYS 0 78 " distance=1.71 Simple disulfide: pdb=" SG CYS 1 701 " - pdb=" SG CYS 1 709 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 1 801 " - " ASN 1 73 " " NAG 1 802 " - " ASN 1 106 " " NAG 1 803 " - " ASN 1 192 " " NAG 7 301 " - " ASN 7 53 " " NAG 7 302 " - " ASN 7 85 " " NAG 7 303 " - " ASN 7 115 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 667.2 milliseconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 41.3% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain '1' and resid 248 through 270 Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 644 through 651 removed outlier: 4.022A pdb=" N ALA 1 649 " --> pdb=" O ALA 1 645 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS 1 650 " --> pdb=" O GLU 1 646 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP 1 651 " --> pdb=" O GLU 1 647 " (cutoff:3.500A) Processing helix chain '1' and resid 726 through 758 Proline residue: 1 746 - end of helix removed outlier: 3.677A pdb=" N LEU 1 753 " --> pdb=" O SER 1 749 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 17 through 22 removed outlier: 3.545A pdb=" N PHE 2 22 " --> pdb=" O TYR 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 39 Processing helix chain '2' and resid 46 through 64 Processing helix chain '2' and resid 66 through 81 Processing helix chain '2' and resid 85 through 99 Processing helix chain '2' and resid 101 through 116 Processing helix chain '2' and resid 122 through 142 removed outlier: 3.785A pdb=" N TYR 2 126 " --> pdb=" O ASP 2 122 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN 2 142 " --> pdb=" O THR 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 158 removed outlier: 3.677A pdb=" N LYS 2 158 " --> pdb=" O ALA 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 162 through 176 Processing helix chain '2' and resid 178 through 193 Processing helix chain '2' and resid 196 through 215 Processing helix chain '2' and resid 217 through 236 removed outlier: 3.903A pdb=" N GLU 2 221 " --> pdb=" O GLN 2 217 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS 2 225 " --> pdb=" O GLU 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 240 through 255 removed outlier: 3.751A pdb=" N GLY 2 255 " --> pdb=" O SER 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 262 through 277 Processing helix chain '2' and resid 278 through 290 Processing helix chain '3' and resid 4 through 34 removed outlier: 3.620A pdb=" N LYS 3 8 " --> pdb=" O ASP 3 4 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU 3 13 " --> pdb=" O TYR 3 9 " (cutoff:3.500A) Proline residue: 3 14 - end of helix removed outlier: 3.597A pdb=" N THR 3 34 " --> pdb=" O MET 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 63 Processing helix chain '3' and resid 64 through 66 No H-bonds generated for 'chain '3' and resid 64 through 66' Processing helix chain '3' and resid 67 through 84 removed outlier: 4.164A pdb=" N ALA 3 73 " --> pdb=" O ASP 3 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU 3 84 " --> pdb=" O LYS 3 80 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 140 removed outlier: 3.876A pdb=" N GLN 3 129 " --> pdb=" O SER 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 153 through 155 No H-bonds generated for 'chain '3' and resid 153 through 155' Processing helix chain '3' and resid 156 through 161 removed outlier: 3.605A pdb=" N GLN 3 161 " --> pdb=" O LYS 3 157 " (cutoff:3.500A) Processing helix chain '3' and resid 175 through 194 removed outlier: 3.858A pdb=" N TRP 3 179 " --> pdb=" O SER 3 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 3 185 " --> pdb=" O PHE 3 181 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN 3 188 " --> pdb=" O VAL 3 184 " (cutoff:3.500A) Proline residue: 3 189 - end of helix Processing helix chain '3' and resid 221 through 234 removed outlier: 3.627A pdb=" N ILE 3 234 " --> pdb=" O ASN 3 230 " (cutoff:3.500A) Processing helix chain '3' and resid 243 through 252 Processing helix chain '4' and resid 7 through 12 removed outlier: 3.556A pdb=" N HIS 4 12 " --> pdb=" O GLU 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 15 through 22 removed outlier: 4.226A pdb=" N ILE 4 19 " --> pdb=" O ASP 4 15 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU 4 20 " --> pdb=" O THR 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 62 through 76 Processing helix chain '4' and resid 83 through 92 Processing helix chain '4' and resid 99 through 116 removed outlier: 4.113A pdb=" N ILE 4 103 " --> pdb=" O GLN 4 99 " (cutoff:3.500A) Proline residue: 4 113 - end of helix Processing helix chain '4' and resid 136 through 163 removed outlier: 4.396A pdb=" N ALA 4 140 " --> pdb=" O GLN 4 136 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE 4 145 " --> pdb=" O MET 4 141 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 31 Processing helix chain '5' and resid 32 through 35 removed outlier: 3.964A pdb=" N LEU 5 35 " --> pdb=" O LEU 5 32 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 32 through 35' Processing helix chain '5' and resid 46 through 66 Processing helix chain '5' and resid 94 through 99 removed outlier: 3.575A pdb=" N THR 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 99 through 106 Processing helix chain '5' and resid 110 through 115 Processing helix chain '5' and resid 121 through 135 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 45 through 68 Processing helix chain '6' and resid 79 through 85 Processing helix chain '6' and resid 88 through 107 Processing helix chain '7' and resid 31 through 35 removed outlier: 3.682A pdb=" N ASN 7 35 " --> pdb=" O ALA 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 42 No H-bonds generated for 'chain '7' and resid 40 through 42' Processing sheet with id=AA1, first strand: chain '0' and resid 51 through 55 removed outlier: 6.612A pdb=" N THR 0 37 " --> pdb=" O VAL 0 53 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE 0 55 " --> pdb=" O LEU 0 35 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU 0 35 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU 0 23 " --> pdb=" O LEU 0 35 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR 0 37 " --> pdb=" O LEU 0 21 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU 0 21 " --> pdb=" O THR 0 37 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER 0 80 " --> pdb=" O LEU 0 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 102 through 109 removed outlier: 3.726A pdb=" N THR 0 117 " --> pdb=" O TYR 0 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 124 through 125 removed outlier: 6.339A pdb=" N GLU 0 124 " --> pdb=" O GLU 1 522 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU 1 509 " --> pdb=" O LEU 1 518 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR 1 520 " --> pdb=" O PHE 1 507 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE 1 507 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU 1 522 " --> pdb=" O ILE 1 505 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 522 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA 1 494 " --> pdb=" O TYR 1 463 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR 1 463 " --> pdb=" O ALA 1 494 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU 1 496 " --> pdb=" O VAL 1 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 35 through 37 removed outlier: 3.763A pdb=" N VAL 1 707 " --> pdb=" O LEU 1 37 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE 1 708 " --> pdb=" O ASP 1 702 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 43 through 48 removed outlier: 6.045A pdb=" N CYS 1 67 " --> pdb=" O VAL 1 84 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL 1 84 " --> pdb=" O CYS 1 67 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL 1 69 " --> pdb=" O ARG 1 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG 1 82 " --> pdb=" O VAL 1 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER 1 71 " --> pdb=" O LEU 1 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 122 through 126 removed outlier: 4.863A pdb=" N LYS 1 114 " --> pdb=" O LEU 1 123 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU 1 125 " --> pdb=" O TRP 1 112 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP 1 112 " --> pdb=" O GLU 1 125 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA 1 101 " --> pdb=" O ASP 1 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 177 through 179 removed outlier: 6.492A pdb=" N SER 1 200 " --> pdb=" O PRO 1 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain '1' and resid 310 through 311 Processing sheet with id=AB1, first strand: chain '1' and resid 333 through 338 removed outlier: 6.694A pdb=" N PHE 1 349 " --> pdb=" O VAL 1 334 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET 1 336 " --> pdb=" O VAL 1 347 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL 1 347 " --> pdb=" O MET 1 336 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP 1 338 " --> pdb=" O GLU 1 345 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLU 1 345 " --> pdb=" O TRP 1 338 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR 1 357 " --> pdb=" O LYS 1 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 379 through 381 removed outlier: 3.772A pdb=" N GLN 1 391 " --> pdb=" O LEU 1 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 379 through 381 Processing sheet with id=AB4, first strand: chain '1' and resid 446 through 451 removed outlier: 6.325A pdb=" N GLY 1 438 " --> pdb=" O THR 1 449 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS 1 451 " --> pdb=" O ILE 1 436 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE 1 436 " --> pdb=" O LYS 1 451 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 1 426 " --> pdb=" O ILE 1 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '1' and resid 475 through 477 Processing sheet with id=AB6, first strand: chain '1' and resid 534 through 537 Processing sheet with id=AB7, first strand: chain '1' and resid 604 through 609 removed outlier: 6.741A pdb=" N GLU 1 624 " --> pdb=" O LYS 1 605 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET 1 607 " --> pdb=" O VAL 1 622 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL 1 622 " --> pdb=" O MET 1 607 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE 1 609 " --> pdb=" O ALA 1 620 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA 1 620 " --> pdb=" O ILE 1 609 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 146 through 147 Processing sheet with id=AB9, first strand: chain '5' and resid 72 through 73 Processing sheet with id=AC1, first strand: chain '7' and resid 23 through 25 removed outlier: 6.179A pdb=" N GLY 7 23 " --> pdb=" O ASN 7 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN 7 77 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 61 through 64 removed outlier: 4.206A pdb=" N ALA 7 122 " --> pdb=" O HIS 7 149 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2382 1.31 - 1.43: 3903 1.43 - 1.56: 8407 1.56 - 1.69: 14 1.69 - 1.81: 112 Bond restraints: 14818 Sorted by residual: bond pdb=" C31 POV 5 201 " pdb=" O31 POV 5 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV 5 201 " pdb=" O21 POV 5 201 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C31 POV 4 201 " pdb=" O31 POV 4 201 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C21 POV 4 201 " pdb=" O21 POV 4 201 " ideal model delta sigma weight residual 1.330 1.428 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O11 POV 5 201 " pdb=" P POV 5 201 " ideal model delta sigma weight residual 1.626 1.693 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 14813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 19695 2.56 - 5.11: 303 5.11 - 7.67: 55 7.67 - 10.22: 12 10.22 - 12.78: 5 Bond angle restraints: 20070 Sorted by residual: angle pdb=" N ALA 4 81 " pdb=" CA ALA 4 81 " pdb=" C ALA 4 81 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" C LEU 4 78 " pdb=" N GLN 4 79 " pdb=" CA GLN 4 79 " ideal model delta sigma weight residual 120.09 126.08 -5.99 1.25e+00 6.40e-01 2.30e+01 angle pdb=" C ASP 1 52 " pdb=" N ARG 1 53 " pdb=" CA ARG 1 53 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C ASN 3 197 " pdb=" N ASP 3 198 " pdb=" CA ASP 3 198 " ideal model delta sigma weight residual 121.56 128.85 -7.29 1.56e+00 4.11e-01 2.18e+01 angle pdb=" N LEU 4 78 " pdb=" CA LEU 4 78 " pdb=" C LEU 4 78 " ideal model delta sigma weight residual 113.23 107.84 5.39 1.24e+00 6.50e-01 1.89e+01 ... (remaining 20065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8205 17.89 - 35.78: 580 35.78 - 53.67: 131 53.67 - 71.56: 31 71.56 - 89.46: 11 Dihedral angle restraints: 8958 sinusoidal: 3740 harmonic: 5218 Sorted by residual: dihedral pdb=" CB CYS 0 65 " pdb=" SG CYS 0 65 " pdb=" SG CYS 0 78 " pdb=" CB CYS 0 78 " ideal model delta sinusoidal sigma weight residual -86.00 -175.46 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CA THR 1 692 " pdb=" C THR 1 692 " pdb=" N ASN 1 693 " pdb=" CA ASN 1 693 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL 3 171 " pdb=" C VAL 3 171 " pdb=" N ARG 3 172 " pdb=" CA ARG 3 172 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 8955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2062 0.080 - 0.160: 225 0.160 - 0.240: 3 0.240 - 0.319: 2 0.319 - 0.399: 3 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG 7 301 " pdb=" ND2 ASN 7 53 " pdb=" C2 NAG 7 301 " pdb=" O5 NAG 7 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG 7 302 " pdb=" ND2 ASN 7 85 " pdb=" C2 NAG 7 302 " pdb=" O5 NAG 7 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG 7 303 " pdb=" ND2 ASN 7 115 " pdb=" C2 NAG 7 303 " pdb=" O5 NAG 7 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2292 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 4 84 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO 4 85 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO 4 85 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 4 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 552 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO 1 553 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO 1 553 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 1 553 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 303 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C ILE 1 303 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE 1 303 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL 1 304 " 0.015 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 133 2.57 - 3.15: 10873 3.15 - 3.73: 22663 3.73 - 4.32: 32906 4.32 - 4.90: 55243 Nonbonded interactions: 121818 Sorted by model distance: nonbonded pdb=" O ASN 1 434 " pdb=" OD1 ASN 1 434 " model vdw 1.983 3.040 nonbonded pdb=" O LEU 3 66 " pdb=" OG1 THR 3 239 " model vdw 2.250 3.040 nonbonded pdb=" O LEU 1 94 " pdb=" OG1 THR 1 133 " model vdw 2.275 3.040 nonbonded pdb=" O ASP 4 15 " pdb=" OD1 ASP 4 15 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU 2 120 " pdb=" CB TYR 2 126 " model vdw 2.293 3.440 ... (remaining 121813 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.100 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.006 0.319 14826 Z= 0.297 Angle : 0.872 20.877 20092 Z= 0.444 Chirality : 0.050 0.399 2295 Planarity : 0.006 0.082 2504 Dihedral : 13.616 86.801 5564 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.87 % Allowed : 8.39 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.16), residues: 1733 helix: -2.06 (0.14), residues: 676 sheet: -1.36 (0.27), residues: 310 loop : -2.88 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 7 129 TYR 0.025 0.002 TYR 1 544 PHE 0.022 0.002 PHE 1 81 TRP 0.020 0.002 TRP 6 52 HIS 0.006 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00576 (14818) covalent geometry : angle 0.83252 (20070) SS BOND : bond 0.22522 ( 2) SS BOND : angle 13.12302 ( 4) hydrogen bonds : bond 0.12958 ( 678) hydrogen bonds : angle 6.65696 ( 1968) link_NAG-ASN : bond 0.01223 ( 6) link_NAG-ASN : angle 6.19466 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 322 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: 0 89 LYS cc_start: 0.8563 (mttm) cc_final: 0.8156 (mtpp) REVERT: 0 99 ASP cc_start: 0.7484 (p0) cc_final: 0.7077 (p0) REVERT: 1 78 GLN cc_start: 0.7510 (mt0) cc_final: 0.7265 (pt0) REVERT: 1 93 GLN cc_start: 0.7256 (mt0) cc_final: 0.7002 (mt0) REVERT: 1 359 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7204 (tp30) REVERT: 1 457 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7870 (mptp) REVERT: 1 500 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6684 (mt-10) REVERT: 1 602 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7417 (mm-30) REVERT: 1 643 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7270 (mppt) REVERT: 1 678 ASN cc_start: 0.7223 (m110) cc_final: 0.6883 (m-40) REVERT: 2 1 MET cc_start: 0.6586 (mmt) cc_final: 0.5651 (ptt) REVERT: 2 39 LYS cc_start: 0.7232 (mttt) cc_final: 0.7022 (tmmt) REVERT: 2 92 LYS cc_start: 0.8154 (tttp) cc_final: 0.7834 (tmtt) REVERT: 2 123 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (p90) REVERT: 2 150 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7782 (mttp) REVERT: 2 153 VAL cc_start: 0.7472 (t) cc_final: 0.7106 (t) REVERT: 2 157 ASP cc_start: 0.6768 (m-30) cc_final: 0.6480 (m-30) REVERT: 3 228 MET cc_start: 0.6480 (tpp) cc_final: 0.6224 (mmt) REVERT: 3 246 GLN cc_start: 0.7864 (pt0) cc_final: 0.6935 (mp-120) REVERT: 4 104 MET cc_start: 0.6528 (tpt) cc_final: 0.4451 (ttm) REVERT: 4 162 MET cc_start: 0.8109 (mtt) cc_final: 0.7819 (mtm) REVERT: 5 124 MET cc_start: 0.7472 (tpt) cc_final: 0.7161 (tpt) outliers start: 14 outliers final: 3 residues processed: 334 average time/residue: 0.5518 time to fit residues: 203.9187 Evaluate side-chains 237 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0270 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 0 104 GLN 1 39 ASN 1 265 ASN 1 521 GLN 1 629 GLN 1 678 ASN 2 21 GLN 3 199 GLN 3 246 GLN 4 4 GLN 4 71 GLN 4 79 GLN 4 167 ASN 6 43 GLN 6 70 GLN 7 100 ASN 7 158 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127097 restraints weight = 16253.807| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.46 r_work: 0.3101 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14826 Z= 0.127 Angle : 0.581 14.376 20092 Z= 0.294 Chirality : 0.043 0.385 2295 Planarity : 0.005 0.064 2504 Dihedral : 8.872 82.460 2092 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.17 % Allowed : 13.92 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.19), residues: 1733 helix: 0.19 (0.18), residues: 682 sheet: -0.90 (0.28), residues: 310 loop : -2.42 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 177 TYR 0.020 0.001 TYR 1 544 PHE 0.013 0.001 PHE 1 81 TRP 0.009 0.001 TRP 1 210 HIS 0.005 0.001 HIS 7 149 Details of bonding type rmsd covalent geometry : bond 0.00284 (14818) covalent geometry : angle 0.56320 (20070) SS BOND : bond 0.00250 ( 2) SS BOND : angle 2.16900 ( 4) hydrogen bonds : bond 0.03709 ( 678) hydrogen bonds : angle 4.94812 ( 1968) link_NAG-ASN : bond 0.00761 ( 6) link_NAG-ASN : angle 4.64985 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7457 (tt0) cc_final: 0.6240 (mt0) REVERT: 0 83 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8581 (ttmt) REVERT: 0 89 LYS cc_start: 0.8408 (mttm) cc_final: 0.8131 (mtpp) REVERT: 0 113 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.6811 (t0) REVERT: 1 78 GLN cc_start: 0.7861 (mt0) cc_final: 0.7277 (pt0) REVERT: 1 93 GLN cc_start: 0.7444 (mt0) cc_final: 0.7234 (mt0) REVERT: 1 95 ASP cc_start: 0.7255 (t0) cc_final: 0.6937 (t70) REVERT: 1 113 GLN cc_start: 0.8813 (mt0) cc_final: 0.8597 (mt0) REVERT: 1 352 ASP cc_start: 0.8145 (m-30) cc_final: 0.7646 (p0) REVERT: 1 359 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7259 (tp30) REVERT: 1 380 ASP cc_start: 0.8447 (t70) cc_final: 0.8155 (t0) REVERT: 1 432 ASP cc_start: 0.8654 (t0) cc_final: 0.8302 (t0) REVERT: 1 457 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7560 (mptp) REVERT: 1 500 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7227 (mp0) REVERT: 1 588 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8238 (pp) REVERT: 1 602 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8221 (mm-30) REVERT: 1 643 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6792 (mttp) REVERT: 1 678 ASN cc_start: 0.8050 (m-40) cc_final: 0.7712 (m-40) REVERT: 2 1 MET cc_start: 0.7199 (mmt) cc_final: 0.5486 (ptt) REVERT: 2 39 LYS cc_start: 0.7253 (mttt) cc_final: 0.6747 (tmmt) REVERT: 2 91 MET cc_start: 0.8834 (mtm) cc_final: 0.8602 (mtm) REVERT: 2 92 LYS cc_start: 0.8266 (tttp) cc_final: 0.7925 (tptt) REVERT: 2 103 LYS cc_start: 0.7478 (mppt) cc_final: 0.6439 (mttt) REVERT: 2 150 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7450 (mttp) REVERT: 2 180 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6788 (mp0) REVERT: 3 30 MET cc_start: 0.7813 (mmt) cc_final: 0.7547 (mmp) REVERT: 3 45 VAL cc_start: 0.7044 (t) cc_final: 0.6825 (m) REVERT: 3 228 MET cc_start: 0.5983 (tpp) cc_final: 0.5747 (mmt) REVERT: 3 246 GLN cc_start: 0.7948 (pt0) cc_final: 0.6786 (mp-120) REVERT: 4 69 GLN cc_start: 0.3375 (mm110) cc_final: 0.2019 (pt0) REVERT: 4 75 GLN cc_start: 0.5547 (mt0) cc_final: 0.5251 (mt0) REVERT: 4 104 MET cc_start: 0.5537 (tpt) cc_final: 0.3776 (ttm) REVERT: 5 50 MET cc_start: 0.7364 (ttt) cc_final: 0.7125 (tmm) REVERT: 5 91 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (mttp) REVERT: 5 124 MET cc_start: 0.7840 (tpt) cc_final: 0.7624 (tpt) REVERT: 7 22 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7690 (mtp180) outliers start: 51 outliers final: 19 residues processed: 281 average time/residue: 0.5233 time to fit residues: 163.0276 Evaluate side-chains 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 209 VAL Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 2 residue 102 ASP Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 0.0270 chunk 126 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.161865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124100 restraints weight = 16442.015| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.58 r_work: 0.3061 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14826 Z= 0.151 Angle : 0.570 14.449 20092 Z= 0.287 Chirality : 0.043 0.370 2295 Planarity : 0.004 0.060 2504 Dihedral : 8.315 80.457 2090 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.73 % Allowed : 15.54 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1733 helix: 0.98 (0.19), residues: 688 sheet: -0.79 (0.28), residues: 309 loop : -2.25 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 384 TYR 0.022 0.001 TYR 1 544 PHE 0.012 0.001 PHE 2 159 TRP 0.010 0.001 TRP 6 52 HIS 0.005 0.001 HIS 7 149 Details of bonding type rmsd covalent geometry : bond 0.00350 (14818) covalent geometry : angle 0.55241 (20070) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.60766 ( 4) hydrogen bonds : bond 0.03583 ( 678) hydrogen bonds : angle 4.72955 ( 1968) link_NAG-ASN : bond 0.00744 ( 6) link_NAG-ASN : angle 4.77828 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: 0 69 GLN cc_start: 0.7375 (tt0) cc_final: 0.6183 (mt0) REVERT: 0 89 LYS cc_start: 0.8388 (mttm) cc_final: 0.8182 (mtpp) REVERT: 0 113 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.6650 (t0) REVERT: 1 51 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7485 (ttp-110) REVERT: 1 78 GLN cc_start: 0.7827 (mt0) cc_final: 0.7285 (pt0) REVERT: 1 95 ASP cc_start: 0.7156 (t0) cc_final: 0.6758 (t70) REVERT: 1 113 GLN cc_start: 0.8653 (mt0) cc_final: 0.8423 (mt0) REVERT: 1 211 GLN cc_start: 0.7691 (tt0) cc_final: 0.7407 (mm-40) REVERT: 1 344 ASP cc_start: 0.7477 (m-30) cc_final: 0.7135 (p0) REVERT: 1 352 ASP cc_start: 0.7987 (m-30) cc_final: 0.7604 (p0) REVERT: 1 359 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7188 (tp30) REVERT: 1 369 SER cc_start: 0.8174 (m) cc_final: 0.7873 (p) REVERT: 1 432 ASP cc_start: 0.8494 (t0) cc_final: 0.8103 (t0) REVERT: 1 457 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7869 (mptp) REVERT: 1 500 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7085 (mt-10) REVERT: 1 570 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: 1 602 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7591 (mm-30) REVERT: 1 643 LYS cc_start: 0.7594 (mmtt) cc_final: 0.6918 (mttp) REVERT: 2 1 MET cc_start: 0.7074 (mmt) cc_final: 0.5550 (ptt) REVERT: 2 39 LYS cc_start: 0.7378 (mttt) cc_final: 0.6781 (tmmt) REVERT: 2 92 LYS cc_start: 0.8162 (tttp) cc_final: 0.7847 (tptt) REVERT: 2 150 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7414 (mtmm) REVERT: 2 157 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6263 (m-30) REVERT: 2 180 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6765 (mp0) REVERT: 2 287 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8262 (tp) REVERT: 3 19 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (mtm) REVERT: 3 30 MET cc_start: 0.7682 (mmt) cc_final: 0.7440 (mmp) REVERT: 3 228 MET cc_start: 0.6058 (tpp) cc_final: 0.5850 (mmt) REVERT: 3 246 GLN cc_start: 0.7964 (pt0) cc_final: 0.6773 (mp-120) REVERT: 3 249 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7655 (mm) REVERT: 4 75 GLN cc_start: 0.5823 (mt0) cc_final: 0.5456 (mt0) REVERT: 4 90 MET cc_start: 0.4601 (pp-130) cc_final: 0.3377 (mtp) REVERT: 4 104 MET cc_start: 0.5547 (tpt) cc_final: 0.3889 (ttm) REVERT: 5 91 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: 5 124 MET cc_start: 0.7784 (tpt) cc_final: 0.7557 (tpt) REVERT: 7 22 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7549 (mtp180) outliers start: 60 outliers final: 20 residues processed: 267 average time/residue: 0.5212 time to fit residues: 154.7490 Evaluate side-chains 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 570 GLU Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 2 residue 157 ASP Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 3 residue 19 MET Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 93 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 4 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123791 restraints weight = 16415.904| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.62 r_work: 0.3046 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14826 Z= 0.167 Angle : 0.573 14.716 20092 Z= 0.289 Chirality : 0.043 0.365 2295 Planarity : 0.004 0.058 2504 Dihedral : 7.945 80.334 2090 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.92 % Allowed : 16.35 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1733 helix: 1.40 (0.19), residues: 690 sheet: -0.70 (0.28), residues: 313 loop : -2.11 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 384 TYR 0.022 0.001 TYR 1 544 PHE 0.013 0.001 PHE 2 51 TRP 0.009 0.001 TRP 4 175 HIS 0.005 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00390 (14818) covalent geometry : angle 0.55708 (20070) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.58353 ( 4) hydrogen bonds : bond 0.03581 ( 678) hydrogen bonds : angle 4.65491 ( 1968) link_NAG-ASN : bond 0.00756 ( 6) link_NAG-ASN : angle 4.57775 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: 0 27 ASP cc_start: 0.7092 (t0) cc_final: 0.6601 (m-30) REVERT: 0 69 GLN cc_start: 0.7796 (tt0) cc_final: 0.6439 (mt0) REVERT: 0 89 LYS cc_start: 0.8421 (mttm) cc_final: 0.8221 (mtpp) REVERT: 0 113 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.6730 (t0) REVERT: 1 51 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7326 (ttp-110) REVERT: 1 78 GLN cc_start: 0.7942 (mt0) cc_final: 0.7324 (pt0) REVERT: 1 95 ASP cc_start: 0.7446 (t0) cc_final: 0.7036 (t70) REVERT: 1 113 GLN cc_start: 0.8841 (mt0) cc_final: 0.8622 (mt0) REVERT: 1 211 GLN cc_start: 0.7707 (tt0) cc_final: 0.7491 (mm-40) REVERT: 1 344 ASP cc_start: 0.7665 (m-30) cc_final: 0.7219 (p0) REVERT: 1 352 ASP cc_start: 0.8208 (m-30) cc_final: 0.7662 (p0) REVERT: 1 359 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7312 (tp30) REVERT: 1 369 SER cc_start: 0.8236 (m) cc_final: 0.7958 (p) REVERT: 1 432 ASP cc_start: 0.8701 (t0) cc_final: 0.8331 (t0) REVERT: 1 457 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7729 (mptp) REVERT: 1 500 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7197 (mp0) REVERT: 1 602 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7881 (mm-30) REVERT: 1 643 LYS cc_start: 0.7615 (mmtt) cc_final: 0.6892 (mttp) REVERT: 2 1 MET cc_start: 0.7357 (mmt) cc_final: 0.5734 (ptt) REVERT: 2 39 LYS cc_start: 0.7427 (mttt) cc_final: 0.6716 (tmmt) REVERT: 2 91 MET cc_start: 0.8866 (mtm) cc_final: 0.8628 (mtm) REVERT: 2 92 LYS cc_start: 0.8397 (tttp) cc_final: 0.8091 (tptt) REVERT: 2 103 LYS cc_start: 0.7516 (mppt) cc_final: 0.6505 (mmtt) REVERT: 2 150 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7416 (mtmm) REVERT: 2 180 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6891 (mp0) REVERT: 2 287 LEU cc_start: 0.8457 (tp) cc_final: 0.8101 (tp) REVERT: 3 30 MET cc_start: 0.7806 (mmt) cc_final: 0.7551 (mmp) REVERT: 3 79 VAL cc_start: 0.6716 (t) cc_final: 0.6464 (m) REVERT: 3 146 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9033 (ptt) REVERT: 3 228 MET cc_start: 0.5967 (tpp) cc_final: 0.5731 (mmt) REVERT: 3 246 GLN cc_start: 0.8066 (pt0) cc_final: 0.6888 (mp-120) REVERT: 3 249 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7609 (mm) REVERT: 4 75 GLN cc_start: 0.5627 (mt0) cc_final: 0.5277 (mt0) REVERT: 4 104 MET cc_start: 0.5212 (tpt) cc_final: 0.3882 (ttm) REVERT: 5 91 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: 5 124 MET cc_start: 0.7835 (tpt) cc_final: 0.7596 (tpt) REVERT: 7 22 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7762 (mtp180) outliers start: 63 outliers final: 33 residues processed: 264 average time/residue: 0.5343 time to fit residues: 156.7271 Evaluate side-chains 258 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 161 LEU Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 254 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 146 MET Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 1 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 93 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 3 138 HIS 4 4 GLN 7 119 GLN 7 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121624 restraints weight = 16354.215| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.60 r_work: 0.3021 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14826 Z= 0.205 Angle : 0.602 14.986 20092 Z= 0.303 Chirality : 0.044 0.361 2295 Planarity : 0.004 0.058 2504 Dihedral : 7.851 80.949 2090 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.29 % Allowed : 16.53 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1733 helix: 1.54 (0.19), residues: 689 sheet: -0.70 (0.29), residues: 313 loop : -2.04 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 105 TYR 0.023 0.002 TYR 1 544 PHE 0.016 0.001 PHE 2 51 TRP 0.010 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00486 (14818) covalent geometry : angle 0.58594 (20070) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.67293 ( 4) hydrogen bonds : bond 0.03720 ( 678) hydrogen bonds : angle 4.69698 ( 1968) link_NAG-ASN : bond 0.00720 ( 6) link_NAG-ASN : angle 4.57741 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: 0 27 ASP cc_start: 0.7032 (t0) cc_final: 0.6583 (m-30) REVERT: 0 69 GLN cc_start: 0.7816 (tt0) cc_final: 0.6479 (mt0) REVERT: 0 113 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6824 (t0) REVERT: 1 78 GLN cc_start: 0.7971 (mt0) cc_final: 0.7319 (pt0) REVERT: 1 95 ASP cc_start: 0.7461 (t0) cc_final: 0.7073 (t70) REVERT: 1 113 GLN cc_start: 0.8848 (mt0) cc_final: 0.8633 (mt0) REVERT: 1 211 GLN cc_start: 0.7761 (tt0) cc_final: 0.7551 (mm-40) REVERT: 1 321 GLN cc_start: 0.8274 (tp40) cc_final: 0.7425 (tm-30) REVERT: 1 344 ASP cc_start: 0.7681 (m-30) cc_final: 0.7291 (p0) REVERT: 1 352 ASP cc_start: 0.8250 (m-30) cc_final: 0.7699 (p0) REVERT: 1 359 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7314 (tp30) REVERT: 1 369 SER cc_start: 0.8292 (m) cc_final: 0.7988 (p) REVERT: 1 380 ASP cc_start: 0.8398 (t70) cc_final: 0.8028 (t0) REVERT: 1 457 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7779 (mptp) REVERT: 1 500 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7211 (mp0) REVERT: 1 522 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: 1 602 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8157 (mm-30) REVERT: 1 643 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6835 (mttp) REVERT: 2 1 MET cc_start: 0.7413 (mmt) cc_final: 0.5784 (ptt) REVERT: 2 29 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7442 (tp40) REVERT: 2 39 LYS cc_start: 0.7431 (mttt) cc_final: 0.6698 (tmmt) REVERT: 2 91 MET cc_start: 0.8846 (mtm) cc_final: 0.8587 (mtm) REVERT: 2 92 LYS cc_start: 0.8369 (tttp) cc_final: 0.8074 (tptt) REVERT: 2 103 LYS cc_start: 0.7661 (mppt) cc_final: 0.6738 (mttt) REVERT: 2 150 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7441 (mtmm) REVERT: 2 180 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6874 (mp0) REVERT: 2 221 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6928 (tp30) REVERT: 2 287 LEU cc_start: 0.8476 (tp) cc_final: 0.8103 (tp) REVERT: 3 30 MET cc_start: 0.7824 (mmt) cc_final: 0.7607 (mmp) REVERT: 3 159 MET cc_start: 0.8770 (ttp) cc_final: 0.8540 (ttp) REVERT: 3 228 MET cc_start: 0.5992 (tpp) cc_final: 0.5744 (mmt) REVERT: 3 246 GLN cc_start: 0.8065 (pt0) cc_final: 0.6912 (mp-120) REVERT: 3 249 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7567 (mm) REVERT: 4 75 GLN cc_start: 0.5672 (mt0) cc_final: 0.5294 (mt0) REVERT: 4 104 MET cc_start: 0.5342 (tpt) cc_final: 0.4022 (ttm) REVERT: 5 91 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (mttm) REVERT: 5 124 MET cc_start: 0.7825 (tpt) cc_final: 0.7609 (tpt) REVERT: 6 22 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7795 (tttm) REVERT: 7 98 ASP cc_start: 0.8778 (m-30) cc_final: 0.8411 (m-30) outliers start: 69 outliers final: 37 residues processed: 268 average time/residue: 0.5428 time to fit residues: 161.5554 Evaluate side-chains 264 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 329 GLU Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 350 SER Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 572 LEU Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 161 LEU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 254 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 162 ILE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 74 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 93 GLN 1 111 HIS ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 4 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.160188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122402 restraints weight = 16342.203| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.47 r_work: 0.3026 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14826 Z= 0.179 Angle : 0.590 14.935 20092 Z= 0.297 Chirality : 0.043 0.358 2295 Planarity : 0.004 0.058 2504 Dihedral : 7.634 80.383 2086 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.98 % Allowed : 17.46 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1733 helix: 1.64 (0.19), residues: 695 sheet: -0.67 (0.29), residues: 311 loop : -2.00 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 22 TYR 0.022 0.001 TYR 1 544 PHE 0.014 0.001 PHE 2 51 TRP 0.011 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00422 (14818) covalent geometry : angle 0.57495 (20070) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.64299 ( 4) hydrogen bonds : bond 0.03608 ( 678) hydrogen bonds : angle 4.65479 ( 1968) link_NAG-ASN : bond 0.00766 ( 6) link_NAG-ASN : angle 4.51883 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: 0 27 ASP cc_start: 0.7083 (t0) cc_final: 0.6601 (m-30) REVERT: 0 69 GLN cc_start: 0.7782 (tt0) cc_final: 0.6544 (mt0) REVERT: 0 89 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7915 (mtmt) REVERT: 0 113 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.6794 (t0) REVERT: 1 78 GLN cc_start: 0.8019 (mt0) cc_final: 0.7383 (pt0) REVERT: 1 95 ASP cc_start: 0.7462 (t0) cc_final: 0.7082 (t70) REVERT: 1 113 GLN cc_start: 0.8787 (mt0) cc_final: 0.8554 (mt0) REVERT: 1 262 ARG cc_start: 0.7693 (ttm170) cc_final: 0.7173 (ttm170) REVERT: 1 321 GLN cc_start: 0.8289 (tp40) cc_final: 0.7478 (tm-30) REVERT: 1 344 ASP cc_start: 0.7751 (m-30) cc_final: 0.7263 (p0) REVERT: 1 352 ASP cc_start: 0.8255 (m-30) cc_final: 0.7721 (p0) REVERT: 1 359 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7248 (tp30) REVERT: 1 369 SER cc_start: 0.8308 (m) cc_final: 0.8030 (p) REVERT: 1 397 GLU cc_start: 0.8238 (tp30) cc_final: 0.7995 (mt-10) REVERT: 1 457 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7812 (mptp) REVERT: 1 467 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7251 (mm-30) REVERT: 1 500 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7240 (mp0) REVERT: 1 522 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: 1 602 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8056 (mm-30) REVERT: 1 643 LYS cc_start: 0.7572 (mmtt) cc_final: 0.6963 (mttp) REVERT: 2 1 MET cc_start: 0.7415 (mmt) cc_final: 0.5803 (ptt) REVERT: 2 29 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7473 (tp40) REVERT: 2 39 LYS cc_start: 0.7443 (mttt) cc_final: 0.6703 (tmmt) REVERT: 2 92 LYS cc_start: 0.8386 (tttp) cc_final: 0.8124 (tptt) REVERT: 2 150 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7474 (mtmm) REVERT: 2 180 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6920 (mp0) REVERT: 2 221 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6900 (tp30) REVERT: 2 253 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: 2 287 LEU cc_start: 0.8518 (tp) cc_final: 0.8149 (tp) REVERT: 3 30 MET cc_start: 0.7802 (mmp) cc_final: 0.7591 (mmp) REVERT: 3 159 MET cc_start: 0.8808 (ttp) cc_final: 0.8586 (ttp) REVERT: 3 228 MET cc_start: 0.5930 (tpp) cc_final: 0.5699 (mmt) REVERT: 3 246 GLN cc_start: 0.8068 (pt0) cc_final: 0.6933 (mp-120) REVERT: 3 249 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7595 (mm) REVERT: 4 71 GLN cc_start: 0.2873 (mt0) cc_final: 0.2092 (mm110) REVERT: 4 75 GLN cc_start: 0.5518 (mt0) cc_final: 0.5257 (mp10) REVERT: 4 104 MET cc_start: 0.5342 (tpt) cc_final: 0.4084 (ttm) REVERT: 4 141 MET cc_start: 0.4382 (ttm) cc_final: 0.3105 (mmp) REVERT: 5 91 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8671 (mttm) REVERT: 5 124 MET cc_start: 0.7823 (tpt) cc_final: 0.7608 (tpt) REVERT: 6 22 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7811 (tttm) REVERT: 7 98 ASP cc_start: 0.8792 (m-30) cc_final: 0.8442 (m-30) REVERT: 7 111 LYS cc_start: 0.8327 (ttpp) cc_final: 0.7586 (tttm) outliers start: 64 outliers final: 35 residues processed: 265 average time/residue: 0.5363 time to fit residues: 158.1645 Evaluate side-chains 260 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 329 GLU Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 350 SER Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 572 LEU Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 161 LEU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 253 GLU Chi-restraints excluded: chain 2 residue 254 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 0.0980 chunk 138 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 93 GLN 1 111 HIS ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 3 246 GLN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124395 restraints weight = 16390.635| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.55 r_work: 0.3069 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14826 Z= 0.133 Angle : 0.567 13.730 20092 Z= 0.286 Chirality : 0.042 0.354 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.350 77.991 2086 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.48 % Allowed : 18.33 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1733 helix: 1.85 (0.20), residues: 694 sheet: -0.68 (0.29), residues: 312 loop : -1.90 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 22 TYR 0.020 0.001 TYR 1 544 PHE 0.011 0.001 PHE 2 51 TRP 0.011 0.001 TRP 1 210 HIS 0.004 0.001 HIS 7 149 Details of bonding type rmsd covalent geometry : bond 0.00305 (14818) covalent geometry : angle 0.54899 (20070) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.62286 ( 4) hydrogen bonds : bond 0.03390 ( 678) hydrogen bonds : angle 4.51082 ( 1968) link_NAG-ASN : bond 0.00792 ( 6) link_NAG-ASN : angle 4.76040 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: 0 69 GLN cc_start: 0.7762 (tt0) cc_final: 0.6484 (mt0) REVERT: 0 89 LYS cc_start: 0.8453 (mtpp) cc_final: 0.7906 (mtmt) REVERT: 0 113 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.6749 (t0) REVERT: 1 78 GLN cc_start: 0.7969 (mt0) cc_final: 0.7347 (pt0) REVERT: 1 95 ASP cc_start: 0.7475 (t0) cc_final: 0.7036 (t70) REVERT: 1 113 GLN cc_start: 0.8822 (mt0) cc_final: 0.8608 (mt0) REVERT: 1 262 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7140 (ttm170) REVERT: 1 321 GLN cc_start: 0.8281 (tp40) cc_final: 0.7471 (tm-30) REVERT: 1 344 ASP cc_start: 0.7687 (m-30) cc_final: 0.7425 (p0) REVERT: 1 352 ASP cc_start: 0.8228 (m-30) cc_final: 0.7673 (p0) REVERT: 1 359 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7191 (mm-30) REVERT: 1 369 SER cc_start: 0.8234 (m) cc_final: 0.7998 (p) REVERT: 1 391 GLN cc_start: 0.7835 (pt0) cc_final: 0.7369 (mt0) REVERT: 1 457 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7728 (mptp) REVERT: 1 500 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7125 (mp0) REVERT: 1 602 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8008 (mm-30) REVERT: 1 643 LYS cc_start: 0.7473 (mmtt) cc_final: 0.6813 (mttp) REVERT: 1 721 MET cc_start: 0.7296 (ttm) cc_final: 0.7060 (mtp) REVERT: 2 1 MET cc_start: 0.7393 (mmt) cc_final: 0.5739 (ptt) REVERT: 2 29 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7442 (tp40) REVERT: 2 39 LYS cc_start: 0.7420 (mttt) cc_final: 0.6656 (tmmt) REVERT: 2 92 LYS cc_start: 0.8440 (tttp) cc_final: 0.8173 (tptt) REVERT: 2 103 LYS cc_start: 0.7589 (mppt) cc_final: 0.6731 (mttt) REVERT: 2 150 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7452 (mtmm) REVERT: 2 180 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6811 (mp0) REVERT: 2 221 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6830 (tp30) REVERT: 2 253 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: 2 287 LEU cc_start: 0.8453 (tp) cc_final: 0.8119 (tp) REVERT: 3 159 MET cc_start: 0.8825 (ttp) cc_final: 0.8618 (ttp) REVERT: 3 228 MET cc_start: 0.5964 (tpp) cc_final: 0.5706 (mmt) REVERT: 3 246 GLN cc_start: 0.7981 (pt0) cc_final: 0.6793 (mp-120) REVERT: 3 249 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7539 (mm) REVERT: 4 71 GLN cc_start: 0.2791 (mt0) cc_final: 0.2095 (mm110) REVERT: 4 75 GLN cc_start: 0.5656 (mt0) cc_final: 0.5445 (mp10) REVERT: 4 104 MET cc_start: 0.5489 (tpt) cc_final: 0.4151 (ttm) REVERT: 4 141 MET cc_start: 0.4316 (ttm) cc_final: 0.3084 (mmp) REVERT: 5 91 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8639 (mttm) REVERT: 5 124 MET cc_start: 0.7818 (tpt) cc_final: 0.7592 (tpt) REVERT: 7 98 ASP cc_start: 0.8748 (m-30) cc_final: 0.8400 (m-30) REVERT: 7 111 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7460 (tttm) outliers start: 56 outliers final: 30 residues processed: 256 average time/residue: 0.5382 time to fit residues: 153.5832 Evaluate side-chains 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 572 LEU Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 159 PHE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 253 GLU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 148 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 111 HIS ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126312 restraints weight = 16265.361| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.62 r_work: 0.3081 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14826 Z= 0.118 Angle : 0.555 13.103 20092 Z= 0.280 Chirality : 0.042 0.351 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.170 76.474 2086 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.92 % Allowed : 19.08 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1733 helix: 2.08 (0.20), residues: 686 sheet: -0.58 (0.29), residues: 310 loop : -1.87 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 22 TYR 0.020 0.001 TYR 1 544 PHE 0.027 0.001 PHE 2 159 TRP 0.011 0.001 TRP 6 52 HIS 0.004 0.001 HIS 7 149 Details of bonding type rmsd covalent geometry : bond 0.00268 (14818) covalent geometry : angle 0.53902 (20070) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.60594 ( 4) hydrogen bonds : bond 0.03269 ( 678) hydrogen bonds : angle 4.42546 ( 1968) link_NAG-ASN : bond 0.00837 ( 6) link_NAG-ASN : angle 4.49863 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: 0 27 ASP cc_start: 0.6889 (t0) cc_final: 0.6416 (m-30) REVERT: 0 41 ASP cc_start: 0.6299 (p0) cc_final: 0.5551 (t0) REVERT: 0 69 GLN cc_start: 0.7764 (tt0) cc_final: 0.6475 (mt0) REVERT: 0 89 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7858 (mtmt) REVERT: 0 113 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.6826 (t0) REVERT: 1 78 GLN cc_start: 0.7962 (mt0) cc_final: 0.7350 (pt0) REVERT: 1 95 ASP cc_start: 0.7384 (t0) cc_final: 0.7005 (t70) REVERT: 1 113 GLN cc_start: 0.8818 (mt0) cc_final: 0.8557 (mt0) REVERT: 1 262 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7106 (ttm170) REVERT: 1 321 GLN cc_start: 0.8243 (tp40) cc_final: 0.7436 (tm-30) REVERT: 1 344 ASP cc_start: 0.7714 (m-30) cc_final: 0.7413 (p0) REVERT: 1 352 ASP cc_start: 0.8195 (m-30) cc_final: 0.7648 (p0) REVERT: 1 359 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7140 (mm-30) REVERT: 1 381 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7978 (m) REVERT: 1 391 GLN cc_start: 0.7789 (pt0) cc_final: 0.7357 (mt0) REVERT: 1 432 ASP cc_start: 0.8697 (t0) cc_final: 0.8286 (t0) REVERT: 1 457 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7547 (mptp) REVERT: 1 500 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7133 (mp0) REVERT: 1 588 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8327 (pp) REVERT: 1 602 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7989 (mm-30) REVERT: 1 643 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6797 (mttp) REVERT: 1 721 MET cc_start: 0.7241 (ttm) cc_final: 0.6982 (mtp) REVERT: 2 1 MET cc_start: 0.7397 (mmt) cc_final: 0.5716 (ptt) REVERT: 2 39 LYS cc_start: 0.7428 (mttt) cc_final: 0.6528 (tmmt) REVERT: 2 92 LYS cc_start: 0.8482 (tttp) cc_final: 0.8149 (tptt) REVERT: 2 103 LYS cc_start: 0.7485 (mppt) cc_final: 0.6692 (mttt) REVERT: 2 150 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7465 (mtmm) REVERT: 2 159 PHE cc_start: 0.7421 (m-80) cc_final: 0.7096 (t80) REVERT: 2 180 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6822 (mp0) REVERT: 2 221 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6806 (tp30) REVERT: 2 253 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: 2 287 LEU cc_start: 0.8478 (tp) cc_final: 0.8158 (tp) REVERT: 3 65 ASN cc_start: 0.8444 (m-40) cc_final: 0.8224 (m-40) REVERT: 3 159 MET cc_start: 0.8842 (ttp) cc_final: 0.8640 (ttp) REVERT: 3 228 MET cc_start: 0.5975 (tpp) cc_final: 0.5732 (mmt) REVERT: 3 246 GLN cc_start: 0.8034 (pt0) cc_final: 0.6837 (mp-120) REVERT: 4 71 GLN cc_start: 0.2803 (mt0) cc_final: 0.2120 (mm110) REVERT: 4 104 MET cc_start: 0.5534 (tpt) cc_final: 0.4292 (ttm) REVERT: 4 141 MET cc_start: 0.4329 (ttm) cc_final: 0.3132 (mmp) REVERT: 5 50 MET cc_start: 0.7835 (ttt) cc_final: 0.7578 (tmm) REVERT: 5 91 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8676 (mttm) REVERT: 5 124 MET cc_start: 0.7779 (tpt) cc_final: 0.7556 (tpt) REVERT: 7 111 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7296 (tttp) outliers start: 47 outliers final: 25 residues processed: 250 average time/residue: 0.5297 time to fit residues: 147.4240 Evaluate side-chains 245 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 253 GLU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 143 MET Chi-restraints excluded: chain 5 residue 19 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 75 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 96 optimal weight: 0.0470 chunk 135 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 111 HIS 1 431 HIS 1 521 GLN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.163942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126487 restraints weight = 16460.856| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.59 r_work: 0.3072 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14826 Z= 0.109 Angle : 0.547 11.583 20092 Z= 0.276 Chirality : 0.041 0.348 2295 Planarity : 0.004 0.057 2504 Dihedral : 6.983 74.777 2086 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.67 % Allowed : 19.45 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1733 helix: 2.21 (0.20), residues: 686 sheet: -0.57 (0.28), residues: 311 loop : -1.82 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 22 TYR 0.019 0.001 TYR 1 544 PHE 0.011 0.001 PHE 1 199 TRP 0.020 0.001 TRP 4 74 HIS 0.003 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00243 (14818) covalent geometry : angle 0.53169 (20070) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.65979 ( 4) hydrogen bonds : bond 0.03167 ( 678) hydrogen bonds : angle 4.32114 ( 1968) link_NAG-ASN : bond 0.00857 ( 6) link_NAG-ASN : angle 4.38626 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6710 (mt0) REVERT: 0 27 ASP cc_start: 0.6753 (t0) cc_final: 0.6349 (m-30) REVERT: 0 41 ASP cc_start: 0.6287 (p0) cc_final: 0.5674 (t0) REVERT: 0 69 GLN cc_start: 0.7708 (tt0) cc_final: 0.6450 (mt0) REVERT: 0 89 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7762 (mtmt) REVERT: 0 90 TYR cc_start: 0.8362 (m-80) cc_final: 0.7823 (m-80) REVERT: 0 113 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6750 (t0) REVERT: 1 67 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8659 (p) REVERT: 1 78 GLN cc_start: 0.7814 (mt0) cc_final: 0.7288 (pt0) REVERT: 1 95 ASP cc_start: 0.7266 (t0) cc_final: 0.6956 (t70) REVERT: 1 113 GLN cc_start: 0.8654 (mt0) cc_final: 0.8390 (mt0) REVERT: 1 262 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7020 (ttm170) REVERT: 1 321 GLN cc_start: 0.8070 (tp40) cc_final: 0.7314 (tm-30) REVERT: 1 359 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7060 (mm-30) REVERT: 1 381 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7810 (m) REVERT: 1 391 GLN cc_start: 0.7549 (pt0) cc_final: 0.7188 (mt0) REVERT: 1 432 ASP cc_start: 0.8502 (t0) cc_final: 0.8111 (t0) REVERT: 1 457 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7498 (mptp) REVERT: 1 500 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6963 (mp0) REVERT: 1 602 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7780 (mm-30) REVERT: 1 643 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6746 (mttp) REVERT: 1 721 MET cc_start: 0.7081 (ttm) cc_final: 0.6844 (mtp) REVERT: 2 1 MET cc_start: 0.7205 (mmt) cc_final: 0.5684 (ptt) REVERT: 2 39 LYS cc_start: 0.7336 (mttt) cc_final: 0.6426 (tmmt) REVERT: 2 54 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (mmp) REVERT: 2 92 LYS cc_start: 0.8375 (tttp) cc_final: 0.8036 (tptt) REVERT: 2 103 LYS cc_start: 0.7368 (mppt) cc_final: 0.6653 (mttt) REVERT: 2 150 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7372 (mtmm) REVERT: 2 180 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6711 (mp0) REVERT: 2 221 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6669 (tp30) REVERT: 2 253 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: 2 287 LEU cc_start: 0.8470 (tp) cc_final: 0.8162 (tp) REVERT: 3 65 ASN cc_start: 0.8428 (m-40) cc_final: 0.8217 (m-40) REVERT: 3 159 MET cc_start: 0.8815 (ttp) cc_final: 0.8583 (ttp) REVERT: 3 228 MET cc_start: 0.5991 (tpp) cc_final: 0.5764 (mmt) REVERT: 3 246 GLN cc_start: 0.7999 (pt0) cc_final: 0.6841 (mp-120) REVERT: 4 71 GLN cc_start: 0.2666 (mt0) cc_final: 0.2384 (mm110) REVERT: 4 75 GLN cc_start: 0.3266 (mp10) cc_final: 0.2795 (mt0) REVERT: 4 104 MET cc_start: 0.5179 (tpt) cc_final: 0.4312 (ttp) REVERT: 5 50 MET cc_start: 0.7636 (ttt) cc_final: 0.7399 (tmm) REVERT: 7 111 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7246 (tttm) outliers start: 43 outliers final: 21 residues processed: 241 average time/residue: 0.5127 time to fit residues: 137.8549 Evaluate side-chains 238 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 2 residue 54 MET Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 253 GLU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 19 SER Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 101 optimal weight: 0.0270 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 111 HIS 4 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.160798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123248 restraints weight = 16319.384| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.66 r_work: 0.3018 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14826 Z= 0.175 Angle : 0.596 11.886 20092 Z= 0.300 Chirality : 0.044 0.349 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.145 78.566 2086 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.24 % Allowed : 20.20 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1733 helix: 2.11 (0.20), residues: 688 sheet: -0.56 (0.28), residues: 310 loop : -1.81 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 43 TYR 0.024 0.001 TYR 1 544 PHE 0.019 0.001 PHE 2 159 TRP 0.016 0.001 TRP 4 74 HIS 0.005 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00413 (14818) covalent geometry : angle 0.58081 (20070) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.60912 ( 4) hydrogen bonds : bond 0.03484 ( 678) hydrogen bonds : angle 4.47121 ( 1968) link_NAG-ASN : bond 0.00795 ( 6) link_NAG-ASN : angle 4.46196 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: 0 69 GLN cc_start: 0.7800 (tt0) cc_final: 0.6460 (mt0) REVERT: 0 85 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7518 (mmt180) REVERT: 0 89 LYS cc_start: 0.8370 (mtpp) cc_final: 0.7781 (mtmt) REVERT: 0 113 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.6903 (t0) REVERT: 1 78 GLN cc_start: 0.7874 (mt0) cc_final: 0.7310 (pt0) REVERT: 1 95 ASP cc_start: 0.7402 (t0) cc_final: 0.7132 (t70) REVERT: 1 110 ASN cc_start: 0.7768 (m-40) cc_final: 0.7531 (m-40) REVERT: 1 197 MET cc_start: 0.8075 (mpt) cc_final: 0.7377 (mpt) REVERT: 1 262 ARG cc_start: 0.7587 (ttm170) cc_final: 0.7067 (ttm170) REVERT: 1 321 GLN cc_start: 0.8129 (tp40) cc_final: 0.7319 (tm-30) REVERT: 1 359 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7087 (mm-30) REVERT: 1 381 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7819 (m) REVERT: 1 391 GLN cc_start: 0.7560 (pt0) cc_final: 0.7191 (mt0) REVERT: 1 457 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7560 (mptp) REVERT: 1 500 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6979 (mp0) REVERT: 1 643 LYS cc_start: 0.7308 (mmtt) cc_final: 0.6737 (mttp) REVERT: 2 1 MET cc_start: 0.7237 (mmt) cc_final: 0.5721 (ptt) REVERT: 2 39 LYS cc_start: 0.7387 (mttt) cc_final: 0.6627 (tmmt) REVERT: 2 92 LYS cc_start: 0.8380 (tttp) cc_final: 0.8037 (tptt) REVERT: 2 103 LYS cc_start: 0.7391 (mppt) cc_final: 0.6667 (mmtt) REVERT: 2 150 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7295 (mtmm) REVERT: 2 180 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6759 (mp0) REVERT: 2 221 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6741 (tp30) REVERT: 2 253 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: 2 287 LEU cc_start: 0.8447 (tp) cc_final: 0.8143 (tp) REVERT: 3 228 MET cc_start: 0.5988 (tpp) cc_final: 0.5758 (mmt) REVERT: 3 246 GLN cc_start: 0.7902 (pt0) cc_final: 0.6765 (mp-120) REVERT: 4 71 GLN cc_start: 0.2900 (mt0) cc_final: 0.2518 (mm110) REVERT: 4 75 GLN cc_start: 0.3287 (mp10) cc_final: 0.2811 (mt0) REVERT: 4 104 MET cc_start: 0.5197 (tpt) cc_final: 0.4293 (ttp) REVERT: 5 50 MET cc_start: 0.7664 (ttt) cc_final: 0.7425 (tmm) REVERT: 7 98 ASP cc_start: 0.8494 (m-30) cc_final: 0.8110 (m-30) REVERT: 7 111 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7243 (tttp) outliers start: 36 outliers final: 25 residues processed: 227 average time/residue: 0.5084 time to fit residues: 128.6020 Evaluate side-chains 231 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 253 GLU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 19 SER Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 170 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 135 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 111 HIS ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126542 restraints weight = 16308.991| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.60 r_work: 0.3058 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14826 Z= 0.124 Angle : 0.565 11.144 20092 Z= 0.284 Chirality : 0.042 0.345 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.005 74.092 2086 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.30 % Allowed : 19.95 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1733 helix: 2.26 (0.20), residues: 681 sheet: -0.58 (0.29), residues: 312 loop : -1.74 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 22 TYR 0.021 0.001 TYR 1 544 PHE 0.011 0.001 PHE 2 51 TRP 0.014 0.001 TRP 4 74 HIS 0.003 0.001 HIS 1 675 Details of bonding type rmsd covalent geometry : bond 0.00284 (14818) covalent geometry : angle 0.55059 (20070) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.63930 ( 4) hydrogen bonds : bond 0.03263 ( 678) hydrogen bonds : angle 4.39581 ( 1968) link_NAG-ASN : bond 0.00882 ( 6) link_NAG-ASN : angle 4.32621 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.99 seconds wall clock time: 101 minutes 9.02 seconds (6069.02 seconds total)