Starting phenix.real_space_refine on Sat Sep 12 07:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb9_21587/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_2026/6wb9_21587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb9_21587/09_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-2.2.1-6174/lib/python3.11/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 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 chiralities: 3 Time building chain proxies: 2.74, per 1000 atoms: 0.19 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: 0.99 Conformation dependent library (CDL) restraints added in 620.9 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: 0.29 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: 2.38 Time building geometry restraints manager: 1.28 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: 8101 17.89 - 35.78: 564 35.78 - 53.67: 117 53.67 - 71.56: 27 71.56 - 89.46: 11 Dihedral angle restraints: 8820 sinusoidal: 3602 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 8817 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: 0.870 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.900 Find NCS groups from input model: 0.050 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:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 13.427 86.801 5426 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/Z covalent geometry : bond 0.00576 / 0.27 (14818) covalent geometry : angle 0.83252 / 0.43 (20070) SS BOND : bond 0.22522 / 11.85 ( 2) SS BOND : angle 13.12302 / 7.43 ( 4) hydrogen bonds : bond 0.12958 / 8.73 ( 678) hydrogen bonds : angle 6.65696 / 4.56 ( 1968) link_NAG-ASN : bond 0.01223 / 0.76 ( 6) link_NAG-ASN : angle 6.19466 / 3.74 ( 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 : 0.532 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: 0.5065 time to fit residues: 187.7613 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 : 0.424 ------------------------------------------------------------------------------- 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... 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 = 0.3783 r_free = 0.3783 target = 0.163649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126197 restraints weight = 16236.690| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.50 r_work: 0.3104 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14826 Z= 0.126 Angle : 0.580 14.607 20092 Z= 0.295 Chirality : 0.043 0.384 2295 Planarity : 0.005 0.063 2504 Dihedral : 7.998 80.519 1954 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.11 % Allowed : 14.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.67 (0.19), residues: 1733 helix: 0.17 (0.18), residues: 682 sheet: -0.91 (0.28), residues: 310 loop : -2.43 (0.21), residues: 741 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 0.013 0.001 PHE 1 81 TRP 0.009 0.001 TRP 1 210 HIS 0.006 0.001 HIS 7 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14818) covalent geometry : angle 0.56334 / 0.29 (20070) SS BOND : bond 0.00678 / 0.35 ( 2) SS BOND : angle 2.07646 / 1.15 ( 4) hydrogen bonds : bond 0.03749 / 2.49 ( 678) hydrogen bonds : angle 4.98461 / 3.40 ( 1968) link_NAG-ASN : bond 0.00723 / 0.44 ( 6) link_NAG-ASN : angle 4.60653 / 2.79 ( 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 304 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7434 (tt0) cc_final: 0.6261 (mt0) REVERT: 0 83 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8549 (ttmt) REVERT: 0 89 LYS cc_start: 0.8451 (mttm) cc_final: 0.8246 (mtpp) REVERT: 0 113 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.6862 (t0) REVERT: 1 26 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7932 (t80) REVERT: 1 78 GLN cc_start: 0.7793 (mt0) cc_final: 0.7270 (pt0) REVERT: 1 93 GLN cc_start: 0.7391 (mt0) cc_final: 0.7173 (mt0) REVERT: 1 95 ASP cc_start: 0.7176 (t0) cc_final: 0.6877 (t70) REVERT: 1 113 GLN cc_start: 0.8698 (mt0) cc_final: 0.8496 (mt0) REVERT: 1 359 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7216 (tp30) REVERT: 1 380 ASP cc_start: 0.8330 (t70) cc_final: 0.8016 (t0) REVERT: 1 429 THR cc_start: 0.9161 (t) cc_final: 0.8960 (t) REVERT: 1 432 ASP cc_start: 0.8441 (t0) cc_final: 0.8098 (t0) REVERT: 1 457 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7604 (mptp) REVERT: 1 500 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7114 (mp0) REVERT: 1 588 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8194 (pp) REVERT: 1 602 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8008 (mm-30) REVERT: 1 643 LYS cc_start: 0.7593 (mmtt) cc_final: 0.6925 (mttp) REVERT: 1 678 ASN cc_start: 0.7822 (m-40) cc_final: 0.7517 (m-40) REVERT: 2 1 MET cc_start: 0.7070 (mmt) cc_final: 0.5565 (ptt) REVERT: 2 39 LYS cc_start: 0.7330 (mttt) cc_final: 0.6839 (tmmt) REVERT: 2 91 MET cc_start: 0.8831 (mtm) cc_final: 0.8603 (mtm) REVERT: 2 92 LYS cc_start: 0.8207 (tttp) cc_final: 0.7792 (tptt) REVERT: 2 103 LYS cc_start: 0.7496 (mppt) cc_final: 0.6428 (mttt) REVERT: 2 150 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7479 (mttp) REVERT: 2 180 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6759 (mp0) REVERT: 3 30 MET cc_start: 0.7681 (mmt) cc_final: 0.7415 (mmp) REVERT: 3 228 MET cc_start: 0.6071 (tpp) cc_final: 0.5822 (mmt) REVERT: 3 246 GLN cc_start: 0.7980 (pt0) cc_final: 0.6820 (mp-120) REVERT: 4 69 GLN cc_start: 0.3426 (mm110) cc_final: 0.2061 (pt0) REVERT: 4 75 GLN cc_start: 0.5717 (mt0) cc_final: 0.5437 (mt0) REVERT: 4 104 MET cc_start: 0.5693 (tpt) cc_final: 0.3842 (ttm) REVERT: 5 50 MET cc_start: 0.7249 (ttt) cc_final: 0.7011 (tmm) REVERT: 5 91 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: 7 22 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7570 (mtp180) outliers start: 50 outliers final: 19 residues processed: 279 average time/residue: 0.5092 time to fit residues: 157.9339 Evaluate side-chains 253 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 123 PHE 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: 5.9990 chunk 58 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 138 HIS 4 4 GLN 7 104 ASN 7 119 GLN 7 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120070 restraints weight = 16489.664| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.79 r_work: 0.2972 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14826 Z= 0.252 Angle : 0.652 15.867 20092 Z= 0.327 Chirality : 0.046 0.368 2295 Planarity : 0.005 0.061 2504 Dihedral : 7.983 84.702 1954 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.92 % Allowed : 15.54 % Favored : 80.55 % 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: -1.16 (0.19), residues: 1733 helix: 0.78 (0.19), residues: 688 sheet: -0.90 (0.28), residues: 312 loop : -2.27 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 384 TYR 0.026 0.002 TYR 1 544 PHE 0.019 0.002 PHE 2 159 TRP 0.011 0.002 TRP 4 175 HIS 0.007 0.001 HIS 1 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (14818) covalent geometry : angle 0.63512 / 0.32 (20070) SS BOND : bond 0.00369 / 0.19 ( 2) SS BOND : angle 0.75571 / 0.37 ( 4) hydrogen bonds : bond 0.04030 / 2.65 ( 678) hydrogen bonds : angle 4.95974 / 3.37 ( 1968) link_NAG-ASN : bond 0.00818 / 0.57 ( 6) link_NAG-ASN : angle 4.98431 / 3.02 ( 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: 63 poor density : 231 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7461 (tt0) cc_final: 0.6317 (mp10) REVERT: 0 89 LYS cc_start: 0.8542 (mttm) cc_final: 0.8136 (mtpp) REVERT: 0 113 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7071 (t0) REVERT: 1 78 GLN cc_start: 0.7910 (mt0) cc_final: 0.7287 (pt0) REVERT: 1 95 ASP cc_start: 0.7392 (t0) cc_final: 0.7033 (t70) REVERT: 1 321 GLN cc_start: 0.8186 (tp40) cc_final: 0.7358 (tm-30) REVERT: 1 344 ASP cc_start: 0.7520 (m-30) cc_final: 0.7162 (p0) REVERT: 1 352 ASP cc_start: 0.8085 (m-30) cc_final: 0.7687 (p0) REVERT: 1 359 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7232 (tp30) REVERT: 1 380 ASP cc_start: 0.8324 (t70) cc_final: 0.7954 (t0) REVERT: 1 457 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7827 (mptp) REVERT: 1 500 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7044 (mp0) REVERT: 1 522 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: 1 602 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7667 (mm-30) REVERT: 1 643 LYS cc_start: 0.7582 (mmtt) cc_final: 0.6902 (mttp) REVERT: 2 1 MET cc_start: 0.7310 (mmt) cc_final: 0.5804 (ptt) REVERT: 2 17 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (mmtm) REVERT: 2 29 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7416 (tp40) REVERT: 2 39 LYS cc_start: 0.7398 (mttt) cc_final: 0.6815 (tmmt) REVERT: 2 92 LYS cc_start: 0.8223 (tttp) cc_final: 0.7890 (tptt) REVERT: 2 150 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7512 (mtmm) REVERT: 2 180 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6872 (mp0) REVERT: 3 30 MET cc_start: 0.7671 (mmt) cc_final: 0.7431 (mmp) REVERT: 3 228 MET cc_start: 0.6020 (tpp) cc_final: 0.5789 (mmt) REVERT: 3 246 GLN cc_start: 0.8008 (pt0) cc_final: 0.6876 (mp-120) REVERT: 3 249 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7659 (mm) REVERT: 4 75 GLN cc_start: 0.5967 (mt0) cc_final: 0.5583 (mt0) REVERT: 4 104 MET cc_start: 0.5734 (tpt) cc_final: 0.4020 (ttm) REVERT: 4 143 MET cc_start: 0.5557 (ttm) cc_final: 0.5342 (ttm) REVERT: 5 91 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8570 (mttm) REVERT: 6 22 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7736 (tttm) REVERT: 6 63 ILE cc_start: 0.9093 (mt) cc_final: 0.8823 (mt) REVERT: 7 22 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7645 (mtp180) REVERT: 7 68 ASP cc_start: 0.8351 (m-30) cc_final: 0.8134 (m-30) REVERT: 7 98 ASP cc_start: 0.8574 (m-30) cc_final: 0.8303 (m-30) outliers start: 63 outliers final: 29 residues processed: 270 average time/residue: 0.4944 time to fit residues: 148.7943 Evaluate side-chains 256 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 387 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 441 ILE Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 522 GLU Chi-restraints excluded: chain 1 residue 572 LEU 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 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 11 ILE 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: 3.9990 chunk 70 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.160414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122866 restraints weight = 16393.909| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.64 r_work: 0.3037 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14826 Z= 0.152 Angle : 0.575 14.552 20092 Z= 0.290 Chirality : 0.043 0.358 2295 Planarity : 0.004 0.059 2504 Dihedral : 7.534 80.681 1954 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.98 % Allowed : 16.10 % Favored : 79.93 % 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: -0.66 (0.20), residues: 1733 helix: 1.35 (0.19), residues: 690 sheet: -0.76 (0.28), residues: 308 loop : -2.10 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 51 TYR 0.021 0.001 TYR 1 544 PHE 0.012 0.001 PHE 2 51 TRP 0.009 0.001 TRP 4 175 HIS 0.005 0.001 HIS 7 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (14818) covalent geometry : angle 0.55826 / 0.29 (20070) SS BOND : bond 0.00275 / 0.14 ( 2) SS BOND : angle 0.58272 / 0.33 ( 4) hydrogen bonds : bond 0.03581 / 2.35 ( 678) hydrogen bonds : angle 4.72153 / 3.22 ( 1968) link_NAG-ASN : bond 0.00796 / 0.50 ( 6) link_NAG-ASN : angle 4.61788 / 2.78 ( 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 294 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 230 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.6948 (t0) cc_final: 0.6471 (m-30) REVERT: 0 69 GLN cc_start: 0.7426 (tt0) cc_final: 0.6279 (mt0) REVERT: 0 113 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6723 (t0) REVERT: 1 78 GLN cc_start: 0.7848 (mt0) cc_final: 0.7279 (pt0) REVERT: 1 93 GLN cc_start: 0.7242 (mt0) cc_final: 0.6963 (mt0) REVERT: 1 95 ASP cc_start: 0.7350 (t0) cc_final: 0.6983 (t70) REVERT: 1 113 GLN cc_start: 0.8726 (mt0) cc_final: 0.8511 (mt0) REVERT: 1 117 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7605 (mp) REVERT: 1 211 GLN cc_start: 0.7681 (tt0) cc_final: 0.7401 (mm-40) REVERT: 1 344 ASP cc_start: 0.7515 (m-30) cc_final: 0.7173 (p0) REVERT: 1 352 ASP cc_start: 0.8005 (m-30) cc_final: 0.7612 (p0) REVERT: 1 359 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7155 (tp30) REVERT: 1 457 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7795 (mptp) REVERT: 1 500 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6978 (mp0) REVERT: 1 602 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7569 (mm-30) REVERT: 1 643 LYS cc_start: 0.7516 (mmtt) cc_final: 0.6871 (mttp) REVERT: 2 1 MET cc_start: 0.7204 (mmt) cc_final: 0.5780 (ptt) REVERT: 2 29 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7368 (tp40) REVERT: 2 39 LYS cc_start: 0.7410 (mttt) cc_final: 0.6756 (tmmt) REVERT: 2 92 LYS cc_start: 0.8170 (tttp) cc_final: 0.7851 (tptt) REVERT: 2 103 LYS cc_start: 0.7571 (mppt) cc_final: 0.6508 (mmtt) REVERT: 2 150 LYS cc_start: 0.7883 (ttmm) cc_final: 0.7424 (mtmm) REVERT: 2 180 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6787 (mp0) REVERT: 2 287 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8153 (tp) REVERT: 3 30 MET cc_start: 0.7691 (mmt) cc_final: 0.7446 (mmp) REVERT: 3 79 VAL cc_start: 0.6725 (t) cc_final: 0.6470 (m) REVERT: 3 146 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8962 (ptt) REVERT: 3 246 GLN cc_start: 0.8009 (pt0) cc_final: 0.6856 (mp-120) REVERT: 3 249 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7613 (mm) REVERT: 4 75 GLN cc_start: 0.5629 (mt0) cc_final: 0.5282 (mt0) REVERT: 4 104 MET cc_start: 0.5328 (tpt) cc_final: 0.3901 (ttm) REVERT: 4 108 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4611 (mpm) REVERT: 4 143 MET cc_start: 0.5555 (ttm) cc_final: 0.5343 (ttm) REVERT: 5 91 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8556 (mttm) REVERT: 7 22 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7624 (mtp180) REVERT: 7 68 ASP cc_start: 0.8226 (m-30) cc_final: 0.7992 (m-30) REVERT: 7 98 ASP cc_start: 0.8544 (m-30) cc_final: 0.8225 (m-30) REVERT: 7 111 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7350 (tttm) REVERT: 7 167 GLN cc_start: 0.6916 (tt0) cc_final: 0.6712 (tt0) outliers start: 64 outliers final: 33 residues processed: 266 average time/residue: 0.4811 time to fit residues: 143.1109 Evaluate side-chains 261 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 117 LEU 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 357 THR 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 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 264 LYS Chi-restraints excluded: chain 2 residue 287 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 108 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=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: 0.9990 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120342 restraints weight = 16324.577| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.64 r_work: 0.2989 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14826 Z= 0.225 Angle : 0.626 15.121 20092 Z= 0.315 Chirality : 0.045 0.355 2295 Planarity : 0.004 0.058 2504 Dihedral : 7.515 82.799 1954 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.16 % Allowed : 16.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.20), residues: 1733 helix: 1.48 (0.19), residues: 689 sheet: -0.79 (0.28), residues: 313 loop : -2.03 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 51 TYR 0.023 0.002 TYR 1 544 PHE 0.016 0.001 PHE 2 51 TRP 0.011 0.002 TRP 6 52 HIS 0.006 0.001 HIS 1 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (14818) covalent geometry : angle 0.61046 / 0.31 (20070) SS BOND : bond 0.00315 / 0.17 ( 2) SS BOND : angle 0.68682 / 0.32 ( 4) hydrogen bonds : bond 0.03833 / 2.50 ( 678) hydrogen bonds : angle 4.78896 / 3.27 ( 1968) link_NAG-ASN : bond 0.00689 / 0.43 ( 6) link_NAG-ASN : angle 4.63447 / 2.80 ( 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 294 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7249 (mp10) REVERT: 0 27 ASP cc_start: 0.6854 (t0) cc_final: 0.6450 (m-30) REVERT: 0 69 GLN cc_start: 0.7661 (tt0) cc_final: 0.6431 (mt0) REVERT: 0 89 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7858 (mtmt) REVERT: 0 113 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7174 (t0) REVERT: 1 78 GLN cc_start: 0.7921 (mt0) cc_final: 0.7305 (pt0) REVERT: 1 93 GLN cc_start: 0.7345 (mt0) cc_final: 0.7078 (mt0) REVERT: 1 95 ASP cc_start: 0.7448 (t0) cc_final: 0.7087 (t70) REVERT: 1 113 GLN cc_start: 0.8721 (mt0) cc_final: 0.8504 (mt0) REVERT: 1 117 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7694 (mp) REVERT: 1 321 GLN cc_start: 0.8185 (tp40) cc_final: 0.7391 (tm-30) REVERT: 1 344 ASP cc_start: 0.7577 (m-30) cc_final: 0.7289 (p0) REVERT: 1 352 ASP cc_start: 0.8096 (m-30) cc_final: 0.7690 (p0) REVERT: 1 357 THR cc_start: 0.8647 (p) cc_final: 0.8412 (p) REVERT: 1 359 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7188 (tp30) REVERT: 1 380 ASP cc_start: 0.8300 (t70) cc_final: 0.7804 (t0) REVERT: 1 397 GLU cc_start: 0.8078 (tp30) cc_final: 0.7803 (mt-10) REVERT: 1 457 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7822 (mptp) REVERT: 1 500 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7071 (mp0) REVERT: 1 602 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7883 (mm-30) REVERT: 1 643 LYS cc_start: 0.7594 (mmtt) cc_final: 0.6976 (mttp) REVERT: 2 1 MET cc_start: 0.7278 (mmt) cc_final: 0.5831 (ptt) REVERT: 2 17 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8336 (mmtm) REVERT: 2 29 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7413 (tp40) REVERT: 2 39 LYS cc_start: 0.7437 (mttt) cc_final: 0.6767 (tmmt) REVERT: 2 92 LYS cc_start: 0.8228 (tttp) cc_final: 0.7917 (tptt) REVERT: 2 150 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7456 (mtmm) REVERT: 2 180 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6834 (mp0) REVERT: 2 221 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6916 (tp30) REVERT: 2 287 LEU cc_start: 0.8531 (tp) cc_final: 0.8243 (tp) REVERT: 3 30 MET cc_start: 0.7714 (mmt) cc_final: 0.7478 (mmp) REVERT: 3 246 GLN cc_start: 0.8016 (pt0) cc_final: 0.6885 (mp-120) REVERT: 3 249 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7627 (mm) REVERT: 4 75 GLN cc_start: 0.5508 (mt0) cc_final: 0.5134 (mt0) REVERT: 4 104 MET cc_start: 0.5367 (tpt) cc_final: 0.3973 (ttm) REVERT: 5 91 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8620 (mttm) REVERT: 6 22 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7706 (tttm) REVERT: 7 57 GLU cc_start: 0.8383 (tt0) cc_final: 0.7849 (tt0) REVERT: 7 98 ASP cc_start: 0.8592 (m-30) cc_final: 0.8245 (m-30) REVERT: 7 111 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7442 (tttp) outliers start: 67 outliers final: 38 residues processed: 268 average time/residue: 0.5118 time to fit residues: 152.8808 Evaluate side-chains 267 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 117 LEU 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 371 SER Chi-restraints excluded: chain 1 residue 387 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 441 ILE 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 1 residue 739 VAL 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 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 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 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: 0.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121467 restraints weight = 16301.919| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.66 r_work: 0.3009 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14826 Z= 0.167 Angle : 0.604 14.835 20092 Z= 0.301 Chirality : 0.043 0.353 2295 Planarity : 0.004 0.059 2504 Dihedral : 7.280 81.052 1954 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.29 % Allowed : 17.34 % Favored : 78.37 % 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: -0.36 (0.20), residues: 1733 helix: 1.71 (0.20), residues: 690 sheet: -0.77 (0.28), residues: 313 loop : -1.97 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 51 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 7 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (14818) covalent geometry : angle 0.57895 / 0.30 (20070) SS BOND : bond 0.00250 / 0.13 ( 2) SS BOND : angle 0.62898 / 0.31 ( 4) hydrogen bonds : bond 0.03578 / 2.33 ( 678) hydrogen bonds : angle 4.66630 / 3.18 ( 1968) link_NAG-ASN : bond 0.00972 / 0.67 ( 6) link_NAG-ASN : angle 5.80539 / 3.60 ( 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 295 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 226 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: 0 27 ASP cc_start: 0.6873 (t0) cc_final: 0.6408 (m-30) REVERT: 0 69 GLN cc_start: 0.7649 (tt0) cc_final: 0.6389 (mt0) REVERT: 0 89 LYS cc_start: 0.8370 (mtpp) cc_final: 0.7739 (mtpt) REVERT: 0 113 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7071 (t0) REVERT: 1 78 GLN cc_start: 0.7882 (mt0) cc_final: 0.7269 (pt0) REVERT: 1 93 GLN cc_start: 0.7279 (mt0) cc_final: 0.6975 (mt0) REVERT: 1 95 ASP cc_start: 0.7433 (t0) cc_final: 0.7099 (t70) REVERT: 1 113 GLN cc_start: 0.8683 (mt0) cc_final: 0.8475 (mt0) REVERT: 1 117 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7611 (mp) REVERT: 1 262 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7075 (ttm170) REVERT: 1 321 GLN cc_start: 0.8141 (tp40) cc_final: 0.7350 (tm-30) REVERT: 1 344 ASP cc_start: 0.7491 (m-30) cc_final: 0.7179 (p0) REVERT: 1 352 ASP cc_start: 0.8049 (m-30) cc_final: 0.7622 (p0) REVERT: 1 359 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7071 (tp30) REVERT: 1 397 GLU cc_start: 0.8036 (tp30) cc_final: 0.7827 (mt-10) REVERT: 1 457 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7787 (mptp) REVERT: 1 500 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6935 (mp0) REVERT: 1 522 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: 1 602 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7839 (mm-30) REVERT: 1 643 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6898 (mttp) REVERT: 2 1 MET cc_start: 0.7208 (mmt) cc_final: 0.5780 (ptt) REVERT: 2 17 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (mmtm) REVERT: 2 29 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7333 (tp40) REVERT: 2 39 LYS cc_start: 0.7423 (mttt) cc_final: 0.6715 (tmmt) REVERT: 2 92 LYS cc_start: 0.8253 (tttp) cc_final: 0.7932 (tptt) REVERT: 2 103 LYS cc_start: 0.7509 (mppt) cc_final: 0.6593 (mttt) REVERT: 2 150 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7364 (mtmm) REVERT: 2 180 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6741 (mp0) REVERT: 2 221 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6813 (tp30) REVERT: 2 253 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: 2 287 LEU cc_start: 0.8488 (tp) cc_final: 0.8117 (tp) REVERT: 3 246 GLN cc_start: 0.7955 (pt0) cc_final: 0.6828 (mp-120) REVERT: 3 249 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7506 (mm) REVERT: 4 71 GLN cc_start: 0.2689 (mt0) cc_final: 0.2478 (mt0) REVERT: 4 75 GLN cc_start: 0.5515 (mt0) cc_final: 0.5217 (mp10) REVERT: 4 104 MET cc_start: 0.5418 (tpt) cc_final: 0.3978 (ttm) REVERT: 4 141 MET cc_start: 0.4435 (ttm) cc_final: 0.3078 (mmp) REVERT: 5 91 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8529 (mttm) REVERT: 6 22 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7638 (tttm) REVERT: 7 57 GLU cc_start: 0.8386 (tt0) cc_final: 0.7843 (tt0) REVERT: 7 98 ASP cc_start: 0.8641 (m-30) cc_final: 0.8261 (m-30) outliers start: 69 outliers final: 33 residues processed: 268 average time/residue: 0.5071 time to fit residues: 151.3008 Evaluate side-chains 256 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 294 LEU 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 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 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 572 LEU 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 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 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: 0.6980 chunk 138 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN 1 111 HIS 1 211 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 3 246 GLN 4 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124706 restraints weight = 16249.659| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.46 r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14826 Z= 0.136 Angle : 0.575 14.235 20092 Z= 0.288 Chirality : 0.042 0.350 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.044 78.892 1954 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.67 % Allowed : 18.27 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.21), residues: 1733 helix: 1.89 (0.20), residues: 688 sheet: -0.72 (0.28), residues: 310 loop : -1.92 (0.23), residues: 735 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 0.012 0.001 PHE 2 51 TRP 0.011 0.001 TRP 6 52 HIS 0.004 0.001 HIS 7 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14818) covalent geometry : angle 0.55444 / 0.28 (20070) SS BOND : bond 0.00224 / 0.12 ( 2) SS BOND : angle 0.63503 / 0.35 ( 4) hydrogen bonds : bond 0.03429 / 2.24 ( 678) hydrogen bonds : angle 4.55514 / 3.11 ( 1968) link_NAG-ASN : bond 0.00678 / 0.33 ( 6) link_NAG-ASN : angle 5.13257 / 3.08 ( 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 278 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: 0 69 GLN cc_start: 0.7824 (tt0) cc_final: 0.6555 (mt0) REVERT: 0 89 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7872 (mtpt) REVERT: 0 113 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.6852 (t0) REVERT: 1 78 GLN cc_start: 0.8035 (mt0) cc_final: 0.7428 (pt0) REVERT: 1 93 GLN cc_start: 0.7407 (mt0) cc_final: 0.7085 (mt0) REVERT: 1 95 ASP cc_start: 0.7601 (t0) cc_final: 0.7219 (t70) REVERT: 1 113 GLN cc_start: 0.8851 (mt0) cc_final: 0.8607 (mt0) REVERT: 1 117 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7703 (mp) REVERT: 1 211 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7313 (mm-40) REVERT: 1 262 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7185 (ttm170) REVERT: 1 321 GLN cc_start: 0.8293 (tp40) cc_final: 0.7540 (tm-30) REVERT: 1 344 ASP cc_start: 0.7746 (m-30) cc_final: 0.7491 (p0) REVERT: 1 352 ASP cc_start: 0.8224 (m-30) cc_final: 0.7718 (p0) REVERT: 1 359 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7247 (mm-30) REVERT: 1 432 ASP cc_start: 0.8722 (t0) cc_final: 0.8347 (t0) REVERT: 1 457 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7872 (mptp) REVERT: 1 500 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7222 (mp0) REVERT: 1 522 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: 1 602 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7937 (mm-30) REVERT: 1 643 LYS cc_start: 0.7546 (mmtt) cc_final: 0.6910 (mttp) REVERT: 1 721 MET cc_start: 0.7375 (ttm) cc_final: 0.7121 (mtp) REVERT: 2 1 MET cc_start: 0.7414 (mmt) cc_final: 0.5824 (ptt) REVERT: 2 29 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7512 (tp40) REVERT: 2 39 LYS cc_start: 0.7410 (mttt) cc_final: 0.6598 (tmmt) REVERT: 2 92 LYS cc_start: 0.8419 (tttp) cc_final: 0.8153 (tptt) REVERT: 2 103 LYS cc_start: 0.7576 (mppt) cc_final: 0.6770 (mmtt) REVERT: 2 150 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7538 (mtmm) REVERT: 2 180 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6926 (mp0) REVERT: 2 221 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6891 (tp30) REVERT: 2 253 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: 2 287 LEU cc_start: 0.8562 (tp) cc_final: 0.8216 (tp) REVERT: 3 246 GLN cc_start: 0.8028 (pt0) cc_final: 0.6848 (mp-120) REVERT: 3 249 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7615 (mm) REVERT: 4 71 GLN cc_start: 0.2828 (mt0) cc_final: 0.2238 (mm110) REVERT: 4 75 GLN cc_start: 0.5608 (mt0) cc_final: 0.5204 (mt0) REVERT: 4 104 MET cc_start: 0.5557 (tpt) cc_final: 0.4237 (ttm) REVERT: 5 50 MET cc_start: 0.7972 (ttt) cc_final: 0.7744 (tmm) REVERT: 5 91 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8696 (mttm) REVERT: 7 98 ASP cc_start: 0.8780 (m-30) cc_final: 0.8425 (m-30) REVERT: 7 111 LYS cc_start: 0.8302 (ttpp) cc_final: 0.7533 (tttp) outliers start: 59 outliers final: 28 residues processed: 256 average time/residue: 0.5145 time to fit residues: 146.7901 Evaluate side-chains 250 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 329 GLU 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 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 123 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 167 GLN 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: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 0.0270 chunk 162 optimal weight: 5.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3766 r_free = 0.3766 target = 0.161988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124552 restraints weight = 16237.033| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.53 r_work: 0.3072 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14826 Z= 0.127 Angle : 0.564 13.467 20092 Z= 0.283 Chirality : 0.042 0.347 2295 Planarity : 0.004 0.057 2504 Dihedral : 6.800 77.797 1950 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.48 % Allowed : 18.83 % Favored : 77.69 % 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: -0.11 (0.21), residues: 1733 helix: 2.00 (0.20), residues: 688 sheet: -0.70 (0.28), residues: 310 loop : -1.88 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 51 TYR 0.020 0.001 TYR 1 544 PHE 0.018 0.001 PHE 1 404 TRP 0.012 0.001 TRP 6 52 HIS 0.006 0.001 HIS 7 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14818) covalent geometry : angle 0.54732 / 0.28 (20070) SS BOND : bond 0.00221 / 0.12 ( 2) SS BOND : angle 0.62482 / 0.36 ( 4) hydrogen bonds : bond 0.03335 / 2.18 ( 678) hydrogen bonds : angle 4.47476 / 3.06 ( 1968) link_NAG-ASN : bond 0.00796 / 0.46 ( 6) link_NAG-ASN : angle 4.55608 / 2.73 ( 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 277 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6789 (mt0) REVERT: 0 69 GLN cc_start: 0.7723 (tt0) cc_final: 0.6435 (mt0) REVERT: 0 89 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8041 (mtpp) REVERT: 0 113 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.6848 (t0) REVERT: 1 78 GLN cc_start: 0.7932 (mt0) cc_final: 0.7310 (pt0) REVERT: 1 93 GLN cc_start: 0.7262 (mt0) cc_final: 0.6988 (mt0) REVERT: 1 95 ASP cc_start: 0.7508 (t0) cc_final: 0.7108 (t70) REVERT: 1 113 GLN cc_start: 0.8780 (mt0) cc_final: 0.8531 (mt0) REVERT: 1 197 MET cc_start: 0.8437 (mpp) cc_final: 0.8200 (mpt) REVERT: 1 262 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7062 (ttm170) REVERT: 1 321 GLN cc_start: 0.8234 (tp40) cc_final: 0.7411 (tm-30) REVERT: 1 344 ASP cc_start: 0.7685 (m-30) cc_final: 0.7394 (p0) REVERT: 1 352 ASP cc_start: 0.8173 (m-30) cc_final: 0.7603 (p0) REVERT: 1 359 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7150 (mm-30) REVERT: 1 391 GLN cc_start: 0.7797 (pt0) cc_final: 0.7326 (mt0) REVERT: 1 432 ASP cc_start: 0.8703 (t0) cc_final: 0.8300 (t0) REVERT: 1 457 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7562 (mptp) REVERT: 1 500 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7140 (mp0) REVERT: 1 522 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: 1 588 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8345 (pp) REVERT: 1 643 LYS cc_start: 0.7345 (mmtt) cc_final: 0.6706 (mttp) REVERT: 2 1 MET cc_start: 0.7382 (mmt) cc_final: 0.5724 (ptt) REVERT: 2 29 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7400 (tp40) REVERT: 2 39 LYS cc_start: 0.7326 (mttt) cc_final: 0.6483 (tmmt) REVERT: 2 92 LYS cc_start: 0.8408 (tttp) cc_final: 0.8096 (tptt) REVERT: 2 103 LYS cc_start: 0.7503 (mppt) cc_final: 0.6786 (mmtt) REVERT: 2 150 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7342 (mtmm) REVERT: 2 157 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: 2 180 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6779 (mp0) REVERT: 2 221 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6786 (tp30) REVERT: 2 287 LEU cc_start: 0.8423 (tp) cc_final: 0.8101 (tp) REVERT: 3 246 GLN cc_start: 0.7942 (pt0) cc_final: 0.6764 (mp-120) REVERT: 3 249 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7493 (mm) REVERT: 4 71 GLN cc_start: 0.2680 (mt0) cc_final: 0.2138 (mm110) REVERT: 4 75 GLN cc_start: 0.5467 (mt0) cc_final: 0.5090 (mt0) REVERT: 4 104 MET cc_start: 0.5445 (tpt) cc_final: 0.4214 (ttm) REVERT: 5 50 MET cc_start: 0.7792 (ttt) cc_final: 0.7580 (tmm) REVERT: 5 91 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8616 (mttm) REVERT: 7 56 THR cc_start: 0.8466 (p) cc_final: 0.8248 (t) REVERT: 7 111 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7285 (tttp) outliers start: 56 outliers final: 31 residues processed: 255 average time/residue: 0.5056 time to fit residues: 143.8639 Evaluate side-chains 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 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 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 157 ASP Chi-restraints excluded: chain 2 residue 212 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 5 residue 19 SER 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 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 167 GLN 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: 3.9990 chunk 120 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN 1 111 HIS 1 431 HIS 1 678 ASN 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 = 0.3769 r_free = 0.3769 target = 0.161969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124604 restraints weight = 16382.039| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.69 r_work: 0.3058 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14826 Z= 0.149 Angle : 0.578 12.323 20092 Z= 0.290 Chirality : 0.043 0.347 2295 Planarity : 0.004 0.057 2504 Dihedral : 6.795 79.066 1950 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.23 % Allowed : 18.89 % 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: -0.08 (0.21), residues: 1733 helix: 1.97 (0.20), residues: 692 sheet: -0.70 (0.28), residues: 311 loop : -1.83 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 51 TYR 0.022 0.001 TYR 1 544 PHE 0.020 0.001 PHE 1 404 TRP 0.012 0.001 TRP 6 52 HIS 0.004 0.001 HIS 1 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14818) covalent geometry : angle 0.56231 / 0.29 (20070) SS BOND : bond 0.00257 / 0.13 ( 2) SS BOND : angle 0.59794 / 0.31 ( 4) hydrogen bonds : bond 0.03407 / 2.23 ( 678) hydrogen bonds : angle 4.48573 / 3.06 ( 1968) link_NAG-ASN : bond 0.00765 / 0.45 ( 6) link_NAG-ASN : angle 4.46478 / 2.68 ( 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 267 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6940 (mt0) REVERT: 0 69 GLN cc_start: 0.7807 (tt0) cc_final: 0.6617 (mt0) REVERT: 0 89 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7774 (mtpt) REVERT: 0 90 TYR cc_start: 0.8398 (m-80) cc_final: 0.7973 (m-80) REVERT: 0 113 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.6985 (t0) REVERT: 1 78 GLN cc_start: 0.7932 (mt0) cc_final: 0.7417 (pt0) REVERT: 1 93 GLN cc_start: 0.7348 (mt0) cc_final: 0.7024 (mt0) REVERT: 1 95 ASP cc_start: 0.7444 (t0) cc_final: 0.7189 (t70) REVERT: 1 113 GLN cc_start: 0.8707 (mt0) cc_final: 0.8452 (mt0) REVERT: 1 262 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7171 (ttm170) REVERT: 1 321 GLN cc_start: 0.8226 (tp40) cc_final: 0.7469 (tm-30) REVERT: 1 352 ASP cc_start: 0.8038 (m-30) cc_final: 0.7690 (p0) REVERT: 1 359 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7201 (mm-30) REVERT: 1 381 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7864 (m) REVERT: 1 391 GLN cc_start: 0.7747 (pt0) cc_final: 0.7319 (mt0) REVERT: 1 432 ASP cc_start: 0.8548 (t0) cc_final: 0.8174 (t0) REVERT: 1 457 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7684 (mptp) REVERT: 1 467 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7165 (mm-30) REVERT: 1 500 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7112 (mp0) REVERT: 1 522 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: 1 588 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8400 (pp) REVERT: 1 643 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6983 (mttp) REVERT: 2 1 MET cc_start: 0.7266 (mmt) cc_final: 0.5830 (ptt) REVERT: 2 29 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7473 (tp40) REVERT: 2 39 LYS cc_start: 0.7357 (mttt) cc_final: 0.6611 (tmmt) REVERT: 2 92 LYS cc_start: 0.8481 (tttp) cc_final: 0.8150 (tptt) REVERT: 2 103 LYS cc_start: 0.7312 (mppt) cc_final: 0.6641 (mmtt) REVERT: 2 150 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7467 (mtmm) REVERT: 2 157 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: 2 180 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6895 (mp0) REVERT: 2 221 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6826 (tp30) REVERT: 2 287 LEU cc_start: 0.8632 (tp) cc_final: 0.8305 (tp) REVERT: 3 53 LEU cc_start: 0.7392 (mp) cc_final: 0.7172 (mp) REVERT: 3 225 MET cc_start: 0.7087 (mtp) cc_final: 0.6796 (mmm) REVERT: 3 246 GLN cc_start: 0.7982 (pt0) cc_final: 0.6873 (mp-120) REVERT: 4 71 GLN cc_start: 0.2836 (mt0) cc_final: 0.2049 (mm110) REVERT: 4 75 GLN cc_start: 0.5749 (mt0) cc_final: 0.5413 (mp10) REVERT: 4 104 MET cc_start: 0.5801 (tpt) cc_final: 0.4546 (ttm) REVERT: 4 141 MET cc_start: 0.4497 (ttm) cc_final: 0.3220 (mmp) REVERT: 5 91 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8639 (mttm) REVERT: 7 111 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7507 (tttp) REVERT: 7 131 TYR cc_start: 0.8926 (m-80) cc_final: 0.8704 (m-80) outliers start: 52 outliers final: 30 residues processed: 249 average time/residue: 0.5021 time to fit residues: 139.3559 Evaluate side-chains 252 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 572 LEU Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 157 ASP Chi-restraints excluded: chain 2 residue 212 LEU 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 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 167 GLN 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: 0.9980 chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN 1 111 HIS 7 81 ASN 7 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.123837 restraints weight = 16236.124| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.58 r_work: 0.3044 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14826 Z= 0.160 Angle : 0.589 12.113 20092 Z= 0.295 Chirality : 0.043 0.347 2295 Planarity : 0.004 0.057 2504 Dihedral : 6.811 79.652 1950 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.80 % Allowed : 19.33 % 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: -0.06 (0.21), residues: 1733 helix: 2.00 (0.20), residues: 687 sheet: -0.71 (0.28), residues: 311 loop : -1.79 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 51 TYR 0.022 0.001 TYR 1 544 PHE 0.019 0.001 PHE 1 404 TRP 0.012 0.001 TRP 6 52 HIS 0.004 0.001 HIS 1 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (14818) covalent geometry : angle 0.57364 / 0.29 (20070) SS BOND : bond 0.00271 / 0.14 ( 2) SS BOND : angle 0.59968 / 0.30 ( 4) hydrogen bonds : bond 0.03452 / 2.25 ( 678) hydrogen bonds : angle 4.51822 / 3.08 ( 1968) link_NAG-ASN : bond 0.00764 / 0.46 ( 6) link_NAG-ASN : angle 4.43081 / 2.66 ( 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 256 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6807 (mt0) REVERT: 0 69 GLN cc_start: 0.7765 (tt0) cc_final: 0.6481 (mt0) REVERT: 0 89 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7664 (mtpt) REVERT: 0 90 TYR cc_start: 0.8455 (m-80) cc_final: 0.8059 (m-80) REVERT: 0 113 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.6889 (t0) REVERT: 1 78 GLN cc_start: 0.7973 (mt0) cc_final: 0.7330 (pt0) REVERT: 1 93 GLN cc_start: 0.7289 (mt0) cc_final: 0.6984 (mt0) REVERT: 1 95 ASP cc_start: 0.7588 (t0) cc_final: 0.7257 (t70) REVERT: 1 113 GLN cc_start: 0.8811 (mt0) cc_final: 0.8558 (mt0) REVERT: 1 197 MET cc_start: 0.8504 (mpp) cc_final: 0.8150 (mpt) REVERT: 1 262 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7055 (ttm170) REVERT: 1 321 GLN cc_start: 0.8258 (tp40) cc_final: 0.7398 (tm-30) REVERT: 1 352 ASP cc_start: 0.8182 (m-30) cc_final: 0.7610 (p0) REVERT: 1 359 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7184 (mm-30) REVERT: 1 381 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7952 (m) REVERT: 1 391 GLN cc_start: 0.7826 (pt0) cc_final: 0.7352 (mt0) REVERT: 1 432 ASP cc_start: 0.8752 (t0) cc_final: 0.8308 (t0) REVERT: 1 457 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7563 (mptp) REVERT: 1 500 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7191 (mp0) REVERT: 1 522 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: 1 588 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8401 (pp) REVERT: 1 643 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6725 (mttp) REVERT: 2 1 MET cc_start: 0.7383 (mmt) cc_final: 0.5699 (ptt) REVERT: 2 29 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7413 (tp40) REVERT: 2 39 LYS cc_start: 0.7329 (mttt) cc_final: 0.6516 (tmmt) REVERT: 2 92 LYS cc_start: 0.8457 (tttp) cc_final: 0.8079 (tptt) REVERT: 2 103 LYS cc_start: 0.7279 (mppt) cc_final: 0.6610 (mmtt) REVERT: 2 150 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7341 (mtmm) REVERT: 2 157 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: 2 180 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6839 (mp0) REVERT: 2 221 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6819 (tp30) REVERT: 2 253 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: 2 287 LEU cc_start: 0.8446 (tp) cc_final: 0.8135 (tp) REVERT: 3 225 MET cc_start: 0.6844 (mtp) cc_final: 0.6593 (mmm) REVERT: 3 246 GLN cc_start: 0.7952 (pt0) cc_final: 0.6780 (mp10) REVERT: 4 71 GLN cc_start: 0.2617 (mt0) cc_final: 0.1916 (mm110) REVERT: 4 75 GLN cc_start: 0.5507 (mt0) cc_final: 0.5251 (mp10) REVERT: 4 104 MET cc_start: 0.5559 (tpt) cc_final: 0.4335 (ttm) REVERT: 4 141 MET cc_start: 0.4319 (ttm) cc_final: 0.3093 (mmp) REVERT: 5 50 MET cc_start: 0.7855 (ttt) cc_final: 0.7633 (tmm) REVERT: 5 91 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8640 (mttm) REVERT: 7 111 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7425 (tttp) outliers start: 45 outliers final: 29 residues processed: 241 average time/residue: 0.5029 time to fit residues: 134.7815 Evaluate side-chains 245 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 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 329 GLU Chi-restraints excluded: chain 1 residue 340 ASP 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 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 572 LEU Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 157 ASP 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 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 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 167 GLN 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: 0.9980 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 135 optimal weight: 0.0010 chunk 126 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN 1 111 HIS 7 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124128 restraints weight = 16249.009| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.53 r_work: 0.3064 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14826 Z= 0.149 Angle : 0.581 11.762 20092 Z= 0.292 Chirality : 0.043 0.346 2295 Planarity : 0.004 0.056 2504 Dihedral : 6.759 79.077 1950 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.55 % Allowed : 19.70 % 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: -0.04 (0.21), residues: 1733 helix: 2.02 (0.20), residues: 690 sheet: -0.70 (0.28), residues: 311 loop : -1.79 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 51 TYR 0.022 0.001 TYR 1 544 PHE 0.014 0.001 PHE 1 404 TRP 0.012 0.001 TRP 6 52 HIS 0.004 0.001 HIS 1 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14818) covalent geometry : angle 0.56622 / 0.29 (20070) SS BOND : bond 0.00265 / 0.14 ( 2) SS BOND : angle 0.62573 / 0.33 ( 4) hydrogen bonds : bond 0.03406 / 2.23 ( 678) hydrogen bonds : angle 4.49015 / 3.06 ( 1968) link_NAG-ASN : bond 0.00787 / 0.47 ( 6) link_NAG-ASN : angle 4.37412 / 2.63 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5362.61 seconds wall clock time: 92 minutes 15.80 seconds (5535.80 seconds total)