Starting phenix.real_space_refine on Tue Dec 31 02:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb9_21587/12_2024/6wb9_21587.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14507 Number of models: 1 Model: "" Number of chains: 12 Chain: "0" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 902 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5275 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 4 Chain: "2" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2377 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "3" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1591 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Chain: "4" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1197 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain breaks: 2 Chain: "5" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Chain: "6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 804 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "7" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1160 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain breaks: 2 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "5" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.64, per 1000 atoms: 0.60 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: 4.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.74 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: 4.93 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2382 1.31 - 1.43: 3903 1.43 - 1.56: 8407 1.56 - 1.69: 14 1.69 - 1.81: 112 Bond restraints: 14818 Sorted by residual: bond pdb=" C31 POV 5 201 " pdb=" O31 POV 5 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV 5 201 " pdb=" O21 POV 5 201 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C31 POV 4 201 " pdb=" O31 POV 4 201 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C21 POV 4 201 " pdb=" O21 POV 4 201 " ideal model delta sigma weight residual 1.330 1.428 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O11 POV 5 201 " pdb=" P POV 5 201 " ideal model delta sigma weight residual 1.626 1.693 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 14813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 19695 2.56 - 5.11: 303 5.11 - 7.67: 55 7.67 - 10.22: 12 10.22 - 12.78: 5 Bond angle restraints: 20070 Sorted by residual: angle pdb=" N ALA 4 81 " pdb=" CA ALA 4 81 " pdb=" C ALA 4 81 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" C LEU 4 78 " pdb=" N GLN 4 79 " pdb=" CA GLN 4 79 " ideal model delta sigma weight residual 120.09 126.08 -5.99 1.25e+00 6.40e-01 2.30e+01 angle pdb=" C ASP 1 52 " pdb=" N ARG 1 53 " pdb=" CA ARG 1 53 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C ASN 3 197 " pdb=" N ASP 3 198 " pdb=" CA ASP 3 198 " ideal model delta sigma weight residual 121.56 128.85 -7.29 1.56e+00 4.11e-01 2.18e+01 angle pdb=" N LEU 4 78 " pdb=" CA LEU 4 78 " pdb=" C LEU 4 78 " ideal model delta sigma weight residual 113.23 107.84 5.39 1.24e+00 6.50e-01 1.89e+01 ... (remaining 20065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8205 17.89 - 35.78: 580 35.78 - 53.67: 131 53.67 - 71.56: 31 71.56 - 89.46: 11 Dihedral angle restraints: 8958 sinusoidal: 3740 harmonic: 5218 Sorted by residual: dihedral pdb=" CB CYS 0 65 " pdb=" SG CYS 0 65 " pdb=" SG CYS 0 78 " pdb=" CB CYS 0 78 " ideal model delta sinusoidal sigma weight residual -86.00 -175.46 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CA THR 1 692 " pdb=" C THR 1 692 " pdb=" N ASN 1 693 " pdb=" CA ASN 1 693 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL 3 171 " pdb=" C VAL 3 171 " pdb=" N ARG 3 172 " pdb=" CA ARG 3 172 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 8955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2062 0.080 - 0.160: 225 0.160 - 0.240: 3 0.240 - 0.319: 2 0.319 - 0.399: 3 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG 7 301 " pdb=" ND2 ASN 7 53 " pdb=" C2 NAG 7 301 " pdb=" O5 NAG 7 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG 7 302 " pdb=" ND2 ASN 7 85 " pdb=" C2 NAG 7 302 " pdb=" O5 NAG 7 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG 7 303 " pdb=" ND2 ASN 7 115 " pdb=" C2 NAG 7 303 " pdb=" O5 NAG 7 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2292 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 4 84 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO 4 85 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO 4 85 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 4 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 552 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO 1 553 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO 1 553 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 1 553 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 303 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C ILE 1 303 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE 1 303 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL 1 304 " 0.015 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 133 2.57 - 3.15: 10873 3.15 - 3.73: 22663 3.73 - 4.32: 32906 4.32 - 4.90: 55243 Nonbonded interactions: 121818 Sorted by model distance: nonbonded pdb=" O ASN 1 434 " pdb=" OD1 ASN 1 434 " model vdw 1.983 3.040 nonbonded pdb=" O LEU 3 66 " pdb=" OG1 THR 3 239 " model vdw 2.250 3.040 nonbonded pdb=" O LEU 1 94 " pdb=" OG1 THR 1 133 " model vdw 2.275 3.040 nonbonded pdb=" O ASP 4 15 " pdb=" OD1 ASP 4 15 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU 2 120 " pdb=" CB TYR 2 126 " model vdw 2.293 3.440 ... (remaining 121813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 14818 Z= 0.375 Angle : 0.833 12.779 20070 Z= 0.431 Chirality : 0.050 0.399 2295 Planarity : 0.006 0.082 2504 Dihedral : 13.616 86.801 5564 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (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 TRP 0.020 0.002 TRP 6 52 HIS 0.006 0.001 HIS 1 675 PHE 0.022 0.002 PHE 1 81 TYR 0.025 0.002 TYR 1 544 ARG 0.003 0.001 ARG 7 129 *********************** 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 : 1.699 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: 0.8094 (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: 1.1634 time to fit residues: 430.5527 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 : 1.561 ------------------------------------------------------------------------------- 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 145 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 0 104 GLN 1 39 ASN 1 265 ASN 1 521 GLN 1 629 GLN 1 678 ASN 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 7 119 GLN 7 121 ASN 7 158 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14818 Z= 0.283 Angle : 0.611 15.586 20070 Z= 0.314 Chirality : 0.045 0.390 2295 Planarity : 0.005 0.065 2504 Dihedral : 9.069 84.965 2092 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.29 % Allowed : 14.17 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1733 helix: 0.04 (0.18), residues: 688 sheet: -1.00 (0.27), residues: 312 loop : -2.45 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 4 175 HIS 0.006 0.001 HIS 7 149 PHE 0.015 0.001 PHE 2 123 TYR 0.023 0.002 TYR 1 544 ARG 0.005 0.000 ARG 7 22 *********************** 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 298 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7459 (tt0) cc_final: 0.6591 (mt0) REVERT: 0 89 LYS cc_start: 0.8562 (mttm) cc_final: 0.8190 (mtpp) REVERT: 0 113 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7053 (t0) REVERT: 1 78 GLN cc_start: 0.7613 (mt0) cc_final: 0.7387 (pt0) REVERT: 1 380 ASP cc_start: 0.8023 (t70) cc_final: 0.7725 (t0) REVERT: 1 400 ASP cc_start: 0.7960 (t0) cc_final: 0.7620 (t0) REVERT: 1 432 ASP cc_start: 0.8035 (t0) cc_final: 0.7703 (t0) REVERT: 1 457 LYS cc_start: 0.8105 (mmtm) cc_final: 0.7898 (mptp) REVERT: 1 500 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6623 (mt-10) REVERT: 1 588 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8216 (pp) REVERT: 1 602 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7402 (mm-30) REVERT: 1 643 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7137 (mttp) REVERT: 1 703 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8449 (mt) REVERT: 2 1 MET cc_start: 0.6817 (mmt) cc_final: 0.5748 (ptt) REVERT: 2 39 LYS cc_start: 0.7267 (mttt) cc_final: 0.6937 (tmmt) REVERT: 2 91 MET cc_start: 0.8765 (mtm) cc_final: 0.8545 (mtm) REVERT: 2 92 LYS cc_start: 0.8063 (tttp) cc_final: 0.7828 (tptt) REVERT: 2 103 LYS cc_start: 0.7599 (mppt) cc_final: 0.6550 (mttt) REVERT: 2 153 VAL cc_start: 0.7499 (t) cc_final: 0.7134 (t) REVERT: 2 157 ASP cc_start: 0.6829 (m-30) cc_final: 0.6507 (m-30) REVERT: 3 228 MET cc_start: 0.6480 (tpp) cc_final: 0.6210 (mmt) REVERT: 3 246 GLN cc_start: 0.7991 (pt0) cc_final: 0.7086 (mp-120) REVERT: 3 249 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7947 (mm) REVERT: 4 69 GLN cc_start: 0.4170 (mm110) cc_final: 0.2750 (pt0) REVERT: 4 75 GLN cc_start: 0.6366 (mt0) cc_final: 0.6069 (mt0) REVERT: 4 104 MET cc_start: 0.6287 (tpt) cc_final: 0.4373 (ttm) REVERT: 5 91 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8419 (mttp) REVERT: 6 63 ILE cc_start: 0.8948 (mt) cc_final: 0.8663 (mt) REVERT: 7 22 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7383 (mtp180) outliers start: 53 outliers final: 22 residues processed: 274 average time/residue: 1.2498 time to fit residues: 379.7331 Evaluate side-chains 249 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 104 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 1 residue 703 LEU 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 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 53 LEU Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 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 86 optimal weight: 6.9990 chunk 48 optimal weight: 0.0170 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 354 HIS 1 678 ASN 2 21 GLN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14818 Z= 0.204 Angle : 0.553 14.323 20070 Z= 0.283 Chirality : 0.043 0.371 2295 Planarity : 0.004 0.060 2504 Dihedral : 8.280 79.937 2088 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.73 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1733 helix: 1.02 (0.19), residues: 686 sheet: -0.80 (0.28), residues: 308 loop : -2.22 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.005 0.001 HIS 7 149 PHE 0.011 0.001 PHE 2 51 TYR 0.021 0.001 TYR 1 544 ARG 0.003 0.000 ARG 7 22 *********************** 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 296 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7375 (tt0) cc_final: 0.6567 (mp10) REVERT: 0 113 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7093 (t0) REVERT: 0 133 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8578 (mmtm) REVERT: 1 93 GLN cc_start: 0.7109 (mt0) cc_final: 0.6814 (mt0) REVERT: 1 380 ASP cc_start: 0.8043 (t70) cc_final: 0.7742 (t0) REVERT: 1 400 ASP cc_start: 0.7873 (t0) cc_final: 0.7543 (t0) REVERT: 1 432 ASP cc_start: 0.7976 (t0) cc_final: 0.7632 (t0) REVERT: 1 457 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7791 (mptp) REVERT: 1 602 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7419 (mm-30) REVERT: 1 643 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7168 (mttp) REVERT: 2 1 MET cc_start: 0.6772 (mmt) cc_final: 0.5723 (ptt) REVERT: 2 39 LYS cc_start: 0.7378 (mttt) cc_final: 0.6895 (tmmt) REVERT: 2 92 LYS cc_start: 0.8115 (tttp) cc_final: 0.7870 (tptt) REVERT: 2 287 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8581 (tp) REVERT: 3 159 MET cc_start: 0.8320 (ptm) cc_final: 0.7933 (ttp) REVERT: 3 228 MET cc_start: 0.6483 (tpp) cc_final: 0.6214 (mmt) REVERT: 3 246 GLN cc_start: 0.7925 (pt0) cc_final: 0.6970 (mp-120) REVERT: 3 249 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7924 (mm) REVERT: 4 75 GLN cc_start: 0.6321 (mt0) cc_final: 0.5914 (mt0) REVERT: 4 90 MET cc_start: 0.5159 (pp-130) cc_final: 0.3907 (mtp) REVERT: 4 104 MET cc_start: 0.6215 (tpt) cc_final: 0.4397 (ttm) REVERT: 4 108 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.5066 (mpm) REVERT: 4 143 MET cc_start: 0.6247 (ttm) cc_final: 0.6024 (ttm) REVERT: 5 91 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (mttm) REVERT: 7 22 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7341 (mtp180) REVERT: 7 57 GLU cc_start: 0.7967 (tt0) cc_final: 0.7575 (tt0) outliers start: 60 outliers final: 21 residues processed: 268 average time/residue: 1.1178 time to fit residues: 334.9193 Evaluate side-chains 243 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 480 ASP Chi-restraints excluded: chain 1 residue 526 SER 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 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 108 MET Chi-restraints excluded: chain 4 residue 146 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 0.0030 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 678 ASN 3 246 GLN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14818 Z= 0.147 Angle : 0.512 12.877 20070 Z= 0.263 Chirality : 0.042 0.363 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.576 76.599 2088 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.54 % Allowed : 17.15 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1733 helix: 1.57 (0.19), residues: 691 sheet: -0.61 (0.29), residues: 304 loop : -2.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 52 HIS 0.004 0.001 HIS 7 149 PHE 0.010 0.001 PHE 2 159 TYR 0.019 0.001 TYR 1 544 ARG 0.005 0.000 ARG 1 51 *********************** 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 295 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: 0 69 GLN cc_start: 0.7390 (tt0) cc_final: 0.6494 (mt0) REVERT: 0 89 LYS cc_start: 0.8515 (mtpp) cc_final: 0.7963 (mtpt) REVERT: 0 113 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.6790 (t0) REVERT: 0 133 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8459 (mmtm) REVERT: 1 93 GLN cc_start: 0.7308 (mt0) cc_final: 0.7042 (mt0) REVERT: 1 380 ASP cc_start: 0.7956 (t70) cc_final: 0.7632 (t0) REVERT: 1 391 GLN cc_start: 0.7474 (pt0) cc_final: 0.7258 (mt0) REVERT: 1 400 ASP cc_start: 0.7793 (t0) cc_final: 0.7484 (t0) REVERT: 1 432 ASP cc_start: 0.7977 (t0) cc_final: 0.7626 (t0) REVERT: 1 457 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7443 (mptp) REVERT: 1 510 ILE cc_start: 0.8473 (pt) cc_final: 0.8047 (tt) REVERT: 1 588 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (pp) REVERT: 1 602 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7420 (mm-30) REVERT: 1 643 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7134 (mttp) REVERT: 2 1 MET cc_start: 0.6835 (mmt) cc_final: 0.5867 (ptt) REVERT: 2 39 LYS cc_start: 0.7364 (mttt) cc_final: 0.6803 (tmmt) REVERT: 2 92 LYS cc_start: 0.8314 (tttp) cc_final: 0.8028 (tptt) REVERT: 2 103 LYS cc_start: 0.7285 (mppt) cc_final: 0.6274 (mmtt) REVERT: 2 287 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8512 (tp) REVERT: 3 228 MET cc_start: 0.6433 (tpp) cc_final: 0.6208 (mmt) REVERT: 3 246 GLN cc_start: 0.7868 (pt0) cc_final: 0.6972 (mp-120) REVERT: 3 249 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7854 (mm) REVERT: 4 75 GLN cc_start: 0.6073 (mt0) cc_final: 0.5746 (mt0) REVERT: 4 104 MET cc_start: 0.6157 (tpt) cc_final: 0.4445 (ttm) REVERT: 4 108 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.5143 (mpm) REVERT: 4 143 MET cc_start: 0.6335 (ttm) cc_final: 0.6122 (ttm) REVERT: 5 91 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8466 (mttp) REVERT: 7 22 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7460 (mtp180) outliers start: 57 outliers final: 22 residues processed: 266 average time/residue: 1.1684 time to fit residues: 346.4597 Evaluate side-chains 249 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 287 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 108 MET Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 123 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 678 ASN 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14818 Z= 0.203 Angle : 0.531 12.296 20070 Z= 0.272 Chirality : 0.042 0.357 2295 Planarity : 0.004 0.071 2504 Dihedral : 7.359 78.585 2086 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.42 % Allowed : 18.09 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1733 helix: 1.82 (0.20), residues: 687 sheet: -0.49 (0.29), residues: 305 loop : -2.04 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 52 HIS 0.004 0.001 HIS 1 675 PHE 0.011 0.001 PHE 2 51 TYR 0.021 0.001 TYR 1 544 ARG 0.005 0.000 ARG 7 43 *********************** 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 285 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: 0 69 GLN cc_start: 0.7559 (tt0) cc_final: 0.6580 (mt0) REVERT: 0 89 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7842 (mtpt) REVERT: 0 113 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.6791 (t0) REVERT: 0 133 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8484 (mmtm) REVERT: 1 93 GLN cc_start: 0.7236 (mt0) cc_final: 0.6941 (mt0) REVERT: 1 391 GLN cc_start: 0.7456 (pt0) cc_final: 0.7254 (mt0) REVERT: 1 400 ASP cc_start: 0.7829 (t0) cc_final: 0.7495 (t0) REVERT: 1 432 ASP cc_start: 0.8021 (t0) cc_final: 0.7685 (t0) REVERT: 1 457 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7407 (mptp) REVERT: 1 602 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7349 (mm-30) REVERT: 1 643 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7101 (mttp) REVERT: 2 1 MET cc_start: 0.6872 (mmt) cc_final: 0.5863 (ptt) REVERT: 2 39 LYS cc_start: 0.7351 (mttt) cc_final: 0.6752 (tmmt) REVERT: 2 92 LYS cc_start: 0.8353 (tttp) cc_final: 0.8090 (tptt) REVERT: 2 253 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: 2 287 LEU cc_start: 0.8902 (tp) cc_final: 0.8550 (tp) REVERT: 3 228 MET cc_start: 0.6450 (tpp) cc_final: 0.6207 (mmt) REVERT: 3 246 GLN cc_start: 0.7941 (pt0) cc_final: 0.7028 (mp-120) REVERT: 3 249 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7842 (mm) REVERT: 4 71 GLN cc_start: 0.3651 (mt0) cc_final: 0.2749 (mm110) REVERT: 4 75 GLN cc_start: 0.5978 (mt0) cc_final: 0.5593 (mp10) REVERT: 4 104 MET cc_start: 0.6137 (tpt) cc_final: 0.4379 (ttm) REVERT: 4 108 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5230 (mpm) REVERT: 4 141 MET cc_start: 0.4880 (ttm) cc_final: 0.3794 (mmp) REVERT: 4 143 MET cc_start: 0.6303 (ttm) cc_final: 0.6067 (ttm) outliers start: 55 outliers final: 31 residues processed: 262 average time/residue: 1.1750 time to fit residues: 344.5962 Evaluate side-chains 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 95 ASP 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 350 SER 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 406 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 2 residue 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 4 residue 108 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 401 HIS 1 431 HIS 4 4 GLN 7 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14818 Z= 0.258 Angle : 0.561 12.416 20070 Z= 0.287 Chirality : 0.043 0.355 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.367 79.022 2086 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.60 % Allowed : 18.09 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1733 helix: 1.90 (0.20), residues: 683 sheet: -0.58 (0.29), residues: 312 loop : -1.94 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 PHE 0.016 0.001 PHE 1 404 TYR 0.022 0.001 TYR 1 544 ARG 0.005 0.000 ARG 7 22 *********************** 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 277 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7615 (tt0) cc_final: 0.6728 (mt0) REVERT: 0 89 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7793 (mtpt) REVERT: 0 113 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7032 (t0) REVERT: 1 93 GLN cc_start: 0.7240 (mt0) cc_final: 0.6922 (mt0) REVERT: 1 262 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7419 (ttm170) REVERT: 1 321 GLN cc_start: 0.7921 (tp40) cc_final: 0.7390 (tm-30) REVERT: 1 380 ASP cc_start: 0.8009 (t70) cc_final: 0.7674 (t0) REVERT: 1 391 GLN cc_start: 0.7496 (pt0) cc_final: 0.7295 (mt0) REVERT: 1 400 ASP cc_start: 0.7842 (t0) cc_final: 0.7481 (t0) REVERT: 1 432 ASP cc_start: 0.8053 (t0) cc_final: 0.7698 (t0) REVERT: 1 457 LYS cc_start: 0.7651 (mmtm) cc_final: 0.7340 (mptp) REVERT: 1 602 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7390 (mm-30) REVERT: 1 643 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7120 (mttp) REVERT: 2 1 MET cc_start: 0.6903 (mmt) cc_final: 0.5889 (ptt) REVERT: 2 39 LYS cc_start: 0.7350 (mttt) cc_final: 0.6816 (tmmt) REVERT: 2 92 LYS cc_start: 0.8331 (tttp) cc_final: 0.8071 (tptt) REVERT: 2 103 LYS cc_start: 0.7516 (mppt) cc_final: 0.6635 (mmtt) REVERT: 2 253 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: 2 287 LEU cc_start: 0.8894 (tp) cc_final: 0.8553 (tp) REVERT: 3 159 MET cc_start: 0.8367 (ttp) cc_final: 0.8153 (ttp) REVERT: 3 246 GLN cc_start: 0.7941 (pt0) cc_final: 0.7013 (mp-120) REVERT: 3 249 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7841 (mm) REVERT: 4 71 GLN cc_start: 0.3663 (mt0) cc_final: 0.2808 (mm110) REVERT: 4 75 GLN cc_start: 0.5962 (mt0) cc_final: 0.5597 (mp10) REVERT: 4 104 MET cc_start: 0.6143 (tpt) cc_final: 0.4393 (ttm) REVERT: 4 108 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.5258 (mpm) REVERT: 4 141 MET cc_start: 0.4845 (ttm) cc_final: 0.3555 (mmp) REVERT: 7 98 ASP cc_start: 0.8413 (m-30) cc_final: 0.8169 (m-30) outliers start: 58 outliers final: 30 residues processed: 257 average time/residue: 1.1536 time to fit residues: 330.2402 Evaluate side-chains 248 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 350 SER Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 516 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR 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 4 residue 108 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 211 GLN 1 521 GLN 4 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14818 Z= 0.212 Angle : 0.546 12.263 20070 Z= 0.279 Chirality : 0.042 0.352 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.223 77.937 2086 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.17 % Allowed : 18.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1733 helix: 1.97 (0.20), residues: 691 sheet: -0.57 (0.28), residues: 306 loop : -1.97 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.004 0.001 HIS 1 675 PHE 0.017 0.001 PHE 1 404 TYR 0.021 0.001 TYR 1 544 ARG 0.006 0.000 ARG 1 51 *********************** 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 267 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7449 (tt0) cc_final: 0.6578 (mt0) REVERT: 0 89 LYS cc_start: 0.8442 (mtpp) cc_final: 0.7804 (mtpt) REVERT: 0 113 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7067 (t0) REVERT: 0 133 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8466 (mmtm) REVERT: 1 93 GLN cc_start: 0.7240 (mt0) cc_final: 0.6945 (mt0) REVERT: 1 262 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7379 (ttm170) REVERT: 1 321 GLN cc_start: 0.7899 (tp40) cc_final: 0.7393 (tm-30) REVERT: 1 380 ASP cc_start: 0.7972 (t70) cc_final: 0.7632 (t0) REVERT: 1 387 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: 1 400 ASP cc_start: 0.7853 (t0) cc_final: 0.7486 (t0) REVERT: 1 432 ASP cc_start: 0.8027 (t0) cc_final: 0.7650 (t0) REVERT: 1 457 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7269 (mptp) REVERT: 1 602 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7260 (mm-30) REVERT: 1 643 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7079 (mttp) REVERT: 1 647 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6919 (mt-10) REVERT: 2 1 MET cc_start: 0.6904 (mmt) cc_final: 0.5885 (ptt) REVERT: 2 39 LYS cc_start: 0.7325 (mttt) cc_final: 0.6770 (tmmt) REVERT: 2 92 LYS cc_start: 0.8345 (tttp) cc_final: 0.8052 (tptt) REVERT: 2 103 LYS cc_start: 0.7371 (mppt) cc_final: 0.6633 (mmtt) REVERT: 2 221 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6207 (tp30) REVERT: 2 253 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: 2 287 LEU cc_start: 0.8896 (tp) cc_final: 0.8563 (tp) REVERT: 3 159 MET cc_start: 0.8320 (ttp) cc_final: 0.8090 (ttp) REVERT: 3 246 GLN cc_start: 0.7932 (pt0) cc_final: 0.7022 (mp-120) REVERT: 3 249 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7853 (mm) REVERT: 4 71 GLN cc_start: 0.3683 (mt0) cc_final: 0.2866 (mm110) REVERT: 4 75 GLN cc_start: 0.6066 (mt0) cc_final: 0.5630 (mp10) REVERT: 4 104 MET cc_start: 0.6127 (tpt) cc_final: 0.4405 (ttm) REVERT: 4 141 MET cc_start: 0.4857 (ttm) cc_final: 0.3587 (mmp) REVERT: 7 98 ASP cc_start: 0.8396 (m-30) cc_final: 0.8146 (m-30) outliers start: 51 outliers final: 28 residues processed: 249 average time/residue: 1.1231 time to fit residues: 311.6876 Evaluate side-chains 244 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 VAL Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 381 SER Chi-restraints excluded: chain 1 residue 387 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR 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 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 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 169 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 4 4 GLN 4 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14818 Z= 0.311 Angle : 0.601 12.138 20070 Z= 0.306 Chirality : 0.044 0.353 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.391 79.390 2086 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1733 helix: 1.91 (0.19), residues: 686 sheet: -0.60 (0.28), residues: 307 loop : -1.93 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.006 0.001 HIS 1 675 PHE 0.020 0.001 PHE 1 404 TYR 0.024 0.002 TYR 1 544 ARG 0.005 0.000 ARG 1 51 *********************** 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 280 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7462 (tt0) cc_final: 0.6583 (mt0) REVERT: 0 89 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8301 (mtpp) REVERT: 0 90 TYR cc_start: 0.8358 (m-80) cc_final: 0.8037 (m-80) REVERT: 0 113 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7141 (t0) REVERT: 1 93 GLN cc_start: 0.7202 (mt0) cc_final: 0.6909 (mt0) REVERT: 1 197 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7589 (mpt) REVERT: 1 262 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7391 (ttm170) REVERT: 1 321 GLN cc_start: 0.7913 (tp40) cc_final: 0.7377 (tm-30) REVERT: 1 380 ASP cc_start: 0.7976 (t70) cc_final: 0.7530 (t0) REVERT: 1 400 ASP cc_start: 0.7880 (t0) cc_final: 0.7502 (t0) REVERT: 1 457 LYS cc_start: 0.7614 (mmtm) cc_final: 0.7335 (mptp) REVERT: 1 522 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: 1 602 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7186 (mm-30) REVERT: 1 643 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7126 (mttp) REVERT: 2 1 MET cc_start: 0.6941 (mmt) cc_final: 0.5939 (ptt) REVERT: 2 29 GLN cc_start: 0.7552 (tp-100) cc_final: 0.7318 (tp40) REVERT: 2 39 LYS cc_start: 0.7355 (mttt) cc_final: 0.6826 (tmmt) REVERT: 2 92 LYS cc_start: 0.8368 (tttp) cc_final: 0.8068 (tptt) REVERT: 2 103 LYS cc_start: 0.7340 (mppt) cc_final: 0.6657 (mttt) REVERT: 2 221 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6213 (tp30) REVERT: 2 253 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: 2 287 LEU cc_start: 0.8893 (tp) cc_final: 0.8566 (tp) REVERT: 3 85 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.4715 (tm-30) REVERT: 3 246 GLN cc_start: 0.7880 (pt0) cc_final: 0.6987 (mp-120) REVERT: 3 249 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7835 (mm) REVERT: 4 71 GLN cc_start: 0.3679 (mt0) cc_final: 0.2880 (mm110) REVERT: 4 75 GLN cc_start: 0.6229 (mt0) cc_final: 0.5764 (mp10) REVERT: 4 104 MET cc_start: 0.5934 (tpt) cc_final: 0.4470 (ttm) REVERT: 4 141 MET cc_start: 0.4842 (ttm) cc_final: 0.3596 (mmp) REVERT: 6 22 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7430 (tttm) REVERT: 7 98 ASP cc_start: 0.8379 (m-30) cc_final: 0.8140 (m-30) outliers start: 56 outliers final: 35 residues processed: 260 average time/residue: 1.2200 time to fit residues: 355.9398 Evaluate side-chains 261 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 197 MET Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 350 SER Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 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 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR 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 253 GLU Chi-restraints excluded: chain 2 residue 254 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 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 143 LEU 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 154 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 111 HIS 7 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14818 Z= 0.194 Angle : 0.561 11.111 20070 Z= 0.287 Chirality : 0.042 0.350 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.412 76.252 2086 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.92 % Allowed : 19.83 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1733 helix: 2.05 (0.20), residues: 690 sheet: -0.58 (0.28), residues: 306 loop : -1.93 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.003 0.001 HIS 1 675 PHE 0.019 0.001 PHE 1 404 TYR 0.021 0.001 TYR 1 544 ARG 0.005 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7517 (tt0) cc_final: 0.6756 (mt0) REVERT: 0 89 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7800 (mtpt) REVERT: 0 113 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7151 (t0) REVERT: 0 133 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8490 (mmtm) REVERT: 1 93 GLN cc_start: 0.7193 (mt0) cc_final: 0.6875 (mt0) REVERT: 1 197 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7792 (mpt) REVERT: 1 262 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7363 (ttm170) REVERT: 1 321 GLN cc_start: 0.7911 (tp40) cc_final: 0.7386 (tm-30) REVERT: 1 380 ASP cc_start: 0.7924 (t70) cc_final: 0.7532 (t0) REVERT: 1 391 GLN cc_start: 0.7990 (mt0) cc_final: 0.7564 (tt0) REVERT: 1 400 ASP cc_start: 0.7876 (t0) cc_final: 0.7505 (t0) REVERT: 1 432 ASP cc_start: 0.8012 (t0) cc_final: 0.7627 (t0) REVERT: 1 457 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7293 (mptp) REVERT: 1 467 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6709 (mm-30) REVERT: 1 602 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7256 (mm-30) REVERT: 1 643 LYS cc_start: 0.7390 (mmtt) cc_final: 0.7021 (mttp) REVERT: 2 1 MET cc_start: 0.6906 (mmt) cc_final: 0.5860 (ptt) REVERT: 2 29 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7307 (tp40) REVERT: 2 39 LYS cc_start: 0.7340 (mttt) cc_final: 0.6804 (tmmt) REVERT: 2 92 LYS cc_start: 0.8350 (tttp) cc_final: 0.8041 (tptt) REVERT: 2 103 LYS cc_start: 0.7215 (mppt) cc_final: 0.6594 (mmtt) REVERT: 2 221 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6205 (tp30) REVERT: 2 253 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: 2 287 LEU cc_start: 0.8890 (tp) cc_final: 0.8568 (tp) REVERT: 3 85 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.4576 (tm-30) REVERT: 3 246 GLN cc_start: 0.7921 (pt0) cc_final: 0.7018 (mp-120) REVERT: 3 249 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7861 (mm) REVERT: 4 5 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: 4 71 GLN cc_start: 0.3697 (mt0) cc_final: 0.2889 (mm110) REVERT: 4 75 GLN cc_start: 0.6129 (mt0) cc_final: 0.5767 (mp10) REVERT: 4 104 MET cc_start: 0.5933 (tpt) cc_final: 0.4520 (ttm) REVERT: 4 141 MET cc_start: 0.4832 (ttm) cc_final: 0.3593 (mmp) REVERT: 4 143 MET cc_start: 0.5671 (ttm) cc_final: 0.5322 (mtp) REVERT: 7 98 ASP cc_start: 0.8316 (m-30) cc_final: 0.8084 (m-30) outliers start: 47 outliers final: 25 residues processed: 241 average time/residue: 1.1395 time to fit residues: 306.0217 Evaluate side-chains 239 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 VAL Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 197 MET Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 2 residue 175 GLU 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 85 GLU Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 5 GLU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE 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 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 78 GLN 1 111 HIS 3 138 HIS 3 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14818 Z= 0.412 Angle : 0.656 11.712 20070 Z= 0.333 Chirality : 0.047 0.352 2295 Planarity : 0.004 0.058 2504 Dihedral : 7.765 79.807 2086 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.49 % Allowed : 20.26 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1733 helix: 1.80 (0.19), residues: 685 sheet: -0.67 (0.28), residues: 308 loop : -1.96 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 1 260 HIS 0.006 0.001 HIS 1 675 PHE 0.022 0.002 PHE 2 159 TYR 0.027 0.002 TYR 1 544 ARG 0.005 0.001 ARG 4 177 ********************** 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 255 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.6717 (t0) cc_final: 0.6468 (m-30) REVERT: 0 69 GLN cc_start: 0.7521 (tt0) cc_final: 0.6669 (mt0) REVERT: 0 83 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8454 (ttpp) REVERT: 0 85 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7566 (mmt180) REVERT: 0 89 LYS cc_start: 0.8541 (mtpp) cc_final: 0.7900 (mtmt) REVERT: 0 113 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7175 (t0) REVERT: 1 93 GLN cc_start: 0.7143 (mt0) cc_final: 0.6813 (mt0) REVERT: 1 197 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7654 (mpt) REVERT: 1 321 GLN cc_start: 0.7922 (tp40) cc_final: 0.7380 (tm-30) REVERT: 1 380 ASP cc_start: 0.7973 (t70) cc_final: 0.7546 (t0) REVERT: 1 457 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7494 (mptp) REVERT: 1 602 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7168 (mm-30) REVERT: 1 643 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7060 (mttp) REVERT: 2 1 MET cc_start: 0.6950 (mmt) cc_final: 0.5984 (ptt) REVERT: 2 29 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7362 (tp40) REVERT: 2 39 LYS cc_start: 0.7369 (mttt) cc_final: 0.6896 (tmmt) REVERT: 2 92 LYS cc_start: 0.8363 (tttp) cc_final: 0.8102 (tptt) REVERT: 2 103 LYS cc_start: 0.7465 (mppt) cc_final: 0.6779 (mttt) REVERT: 2 221 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6273 (tp30) REVERT: 2 287 LEU cc_start: 0.8888 (tp) cc_final: 0.8556 (tp) REVERT: 3 53 LEU cc_start: 0.7851 (mp) cc_final: 0.7575 (mp) REVERT: 3 85 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.4683 (tm-30) REVERT: 3 146 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8892 (ptt) REVERT: 3 246 GLN cc_start: 0.7990 (pt0) cc_final: 0.7083 (mp-120) REVERT: 3 249 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7899 (mm) REVERT: 4 71 GLN cc_start: 0.3685 (mt0) cc_final: 0.2860 (mm110) REVERT: 4 75 GLN cc_start: 0.6257 (mt0) cc_final: 0.5873 (mp10) REVERT: 4 104 MET cc_start: 0.5911 (tpt) cc_final: 0.4648 (ttm) REVERT: 4 141 MET cc_start: 0.4868 (ttm) cc_final: 0.3622 (mmp) REVERT: 6 22 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7442 (tttm) REVERT: 7 98 ASP cc_start: 0.8384 (m-30) cc_final: 0.8171 (m-30) outliers start: 40 outliers final: 24 residues processed: 239 average time/residue: 1.1463 time to fit residues: 304.9462 Evaluate side-chains 236 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 197 MET Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 85 GLU 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 5 residue 76 ILE 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 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 140 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 111 HIS 3 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123564 restraints weight = 16331.456| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.70 r_work: 0.3037 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14818 Z= 0.200 Angle : 0.567 10.760 20070 Z= 0.290 Chirality : 0.043 0.382 2295 Planarity : 0.004 0.057 2504 Dihedral : 7.404 74.953 2086 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.11 % Allowed : 21.07 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1733 helix: 1.96 (0.20), residues: 690 sheet: -0.62 (0.29), residues: 304 loop : -1.93 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.007 0.001 HIS 1 675 PHE 0.021 0.001 PHE 1 404 TYR 0.022 0.001 TYR 1 544 ARG 0.005 0.000 ARG 7 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5563.05 seconds wall clock time: 101 minutes 17.47 seconds (6077.47 seconds total)