Starting phenix.real_space_refine on Tue Dec 31 07:14:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqr_23950/12_2024/7mqr_23950.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9416 2.51 5 N 2518 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 14878 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "E" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "J" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.34, per 1000 atoms: 0.56 Number of scatterers: 14878 At special positions: 0 Unit cell: (94.185, 151.515, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2824 8.00 N 2518 7.00 C 9416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.04 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.02 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.96 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.10 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.09 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS H 19 " distance=2.10 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.04 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=1.97 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS J 19 " distance=1.97 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " 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 E1001 " - " ASN E 255 " " NAG E1002 " - " ASN E 25 " " NAG E1003 " - " ASN E 215 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 606 " " NAG E1006 " - " ASN E 624 " " NAG E1007 " - " ASN E 397 " " NAG E1008 " - " ASN E 337 " " NAG E1009 " - " ASN E 418 " " NAG E1010 " - " ASN E 111 " " NAG F1001 " - " ASN F 255 " " NAG F1002 " - " ASN F 25 " " NAG F1003 " - " ASN F 215 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 606 " " NAG F1006 " - " ASN F 624 " " NAG F1007 " - " ASN F 397 " " NAG F1008 " - " ASN F 337 " " NAG F1009 " - " ASN F 418 " " NAG F1010 " - " ASN F 111 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 18.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 17 removed outlier: 4.034A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 23 removed outlier: 4.338A pdb=" N ARG E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.583A pdb=" N PHE E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP E 142 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 143 " --> pdb=" O VAL E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 143' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 435 through 447 Processing helix chain 'E' and resid 496 through 500 Processing helix chain 'E' and resid 692 through 714 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.033A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 18 Processing helix chain 'F' and resid 16 through 23 removed outlier: 4.339A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.584A pdb=" N PHE F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP F 74 " --> pdb=" O SER F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP F 142 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O VAL F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 139 through 143' Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 350 through 358 Processing helix chain 'F' and resid 435 through 447 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 692 through 714 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU E 36 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 117 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL E 146 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 119 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.710A pdb=" N ILE E 57 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'E' and resid 212 through 216 removed outlier: 5.504A pdb=" N LEU E 213 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS E 228 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 215 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.960A pdb=" N HIS E 247 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LYS E 369 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'E' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 588 " --> pdb=" O TYR E 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE E 602 " --> pdb=" O LYS E 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 614 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 604 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 788 " --> pdb=" O ARG E 794 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 803 " --> pdb=" O TYR E 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 818 through 822 Processing sheet with id=AB6, first strand: chain 'E' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 884 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 901 " --> pdb=" O VAL E 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU F 36 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 117 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL F 146 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 119 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.708A pdb=" N ILE F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 82 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'F' and resid 212 through 216 removed outlier: 5.503A pdb=" N LEU F 213 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS F 228 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN F 215 " --> pdb=" O VAL F 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.961A pdb=" N HIS F 247 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS F 369 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 340 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG F 371 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE F 342 " --> pdb=" O ARG F 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 485 through 487 Processing sheet with id=AC7, first strand: chain 'F' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL F 588 " --> pdb=" O TYR F 562 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE F 602 " --> pdb=" O LYS F 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 614 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 604 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 788 " --> pdb=" O ARG F 794 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 803 " --> pdb=" O TYR F 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 818 through 822 Processing sheet with id=AD3, first strand: chain 'F' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 884 " --> pdb=" O THR F 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 901 " --> pdb=" O VAL F 884 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 954 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: 5.50 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4812 1.35 - 1.48: 3842 1.48 - 1.61: 6422 1.61 - 1.74: 0 1.74 - 1.87: 142 Bond restraints: 15218 Sorted by residual: bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 NAG E1001 " pdb=" O5 NAG E1001 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C1 NAG E1007 " pdb=" O5 NAG E1007 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.23e+01 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 20523 7.08 - 14.16: 97 14.16 - 21.25: 6 21.25 - 28.33: 2 28.33 - 35.41: 2 Bond angle restraints: 20630 Sorted by residual: angle pdb=" CG ARG F 774 " pdb=" CD ARG F 774 " pdb=" NE ARG F 774 " ideal model delta sigma weight residual 112.00 135.38 -23.38 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CG ARG E 774 " pdb=" CD ARG E 774 " pdb=" NE ARG E 774 " ideal model delta sigma weight residual 112.00 135.33 -23.33 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CA LEU J 15 " pdb=" CB LEU J 15 " pdb=" CG LEU J 15 " ideal model delta sigma weight residual 116.30 151.71 -35.41 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA LEU H 15 " pdb=" CB LEU H 15 " pdb=" CG LEU H 15 " ideal model delta sigma weight residual 116.30 151.66 -35.36 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA GLU C 17 " pdb=" CB GLU C 17 " pdb=" CG GLU C 17 " ideal model delta sigma weight residual 114.10 130.19 -16.09 2.00e+00 2.50e-01 6.48e+01 ... (remaining 20625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 8671 21.73 - 43.47: 708 43.47 - 65.20: 95 65.20 - 86.93: 28 86.93 - 108.67: 16 Dihedral angle restraints: 9518 sinusoidal: 4220 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS G 20 " pdb=" SG CYS G 20 " pdb=" SG CYS H 19 " pdb=" CB CYS H 19 " ideal model delta sinusoidal sigma weight residual -86.00 -167.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS I 20 " pdb=" SG CYS I 20 " pdb=" SG CYS J 19 " pdb=" CB CYS J 19 " ideal model delta sinusoidal sigma weight residual -86.00 -165.10 79.10 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA THR F 578 " pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta harmonic sigma weight residual 180.00 136.61 43.39 0 5.00e+00 4.00e-02 7.53e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1994 0.099 - 0.198: 274 0.198 - 0.297: 42 0.297 - 0.396: 6 0.396 - 0.494: 4 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CB ILE E 370 " pdb=" CA ILE E 370 " pdb=" CG1 ILE E 370 " pdb=" CG2 ILE E 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB VAL H 18 " pdb=" CA VAL H 18 " pdb=" CG1 VAL H 18 " pdb=" CG2 VAL H 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2317 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C VAL H 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL H 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU H 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C VAL J 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL J 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU J 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 285 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO F 286 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 286 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 286 " -0.035 5.00e-02 4.00e+02 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5057 2.89 - 3.39: 12078 3.39 - 3.89: 25071 3.89 - 4.40: 26394 4.40 - 4.90: 44720 Nonbonded interactions: 113320 Sorted by model distance: nonbonded pdb=" O SER E 700 " pdb=" OG1 THR E 704 " model vdw 2.382 3.040 nonbonded pdb=" O SER F 700 " pdb=" OG1 THR F 704 " model vdw 2.382 3.040 nonbonded pdb=" O LYS E 310 " pdb=" OG1 THR E 334 " model vdw 2.394 3.040 nonbonded pdb=" O LYS F 310 " pdb=" OG1 THR F 334 " model vdw 2.394 3.040 nonbonded pdb=" OG1 THR E 889 " pdb=" OD1 ASN E 894 " model vdw 2.401 3.040 ... (remaining 113315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'B' and resid 5 through 20) selection = (chain 'D' and resid 5 through 20) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.050 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.007 0.102 15218 Z= 0.487 Angle : 1.323 35.411 20630 Z= 0.660 Chirality : 0.072 0.494 2320 Planarity : 0.007 0.064 2632 Dihedral : 15.731 108.669 5950 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 0.60 % Allowed : 0.85 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.42 (0.17), residues: 1770 helix: -3.96 (0.17), residues: 256 sheet: -1.15 (0.28), residues: 328 loop : -2.34 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 832 HIS 0.008 0.001 HIS F 775 PHE 0.035 0.003 PHE E 497 TYR 0.023 0.002 TYR I 14 ARG 0.012 0.001 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: E 442 MET cc_start: 0.8940 (ttp) cc_final: 0.8648 (tmm) REVERT: E 831 MET cc_start: 0.9581 (mmp) cc_final: 0.9364 (mmp) REVERT: C 17 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: H 15 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9049 (tp) REVERT: F 556 LEU cc_start: 0.8895 (mp) cc_final: 0.8672 (mp) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.2453 time to fit residues: 40.7063 Evaluate side-chains 75 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 0.0980 chunk 159 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 15 GLN E 108 ASN E 143 ASN E 295 ASN E 710 HIS C 5 GLN C 15 GLN F 143 ASN F 295 ASN F 710 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15218 Z= 0.196 Angle : 0.648 8.451 20630 Z= 0.337 Chirality : 0.047 0.202 2320 Planarity : 0.005 0.058 2632 Dihedral : 9.642 88.326 2396 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.28 % Rotamer: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 1770 helix: -2.46 (0.26), residues: 264 sheet: -0.66 (0.29), residues: 328 loop : -2.02 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 414 HIS 0.009 0.001 HIS E 775 PHE 0.015 0.001 PHE F 565 TYR 0.016 0.001 TYR E 91 ARG 0.007 0.000 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 ILE cc_start: 0.8274 (mm) cc_final: 0.7718 (tp) REVERT: H 13 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7304 (tt0) REVERT: J 13 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7546 (tm-30) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.2120 time to fit residues: 33.6469 Evaluate side-chains 59 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 264 HIS E 328 GLN C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN F 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15218 Z= 0.190 Angle : 0.609 7.783 20630 Z= 0.312 Chirality : 0.046 0.189 2320 Planarity : 0.004 0.041 2632 Dihedral : 7.649 68.174 2396 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.18 % Favored : 92.60 % Rotamer: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1770 helix: -1.21 (0.30), residues: 254 sheet: -0.51 (0.29), residues: 318 loop : -1.70 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 414 HIS 0.005 0.001 HIS I 21 PHE 0.012 0.001 PHE E 89 TYR 0.014 0.001 TYR F 91 ARG 0.004 0.000 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.9258 (mm) cc_final: 0.9008 (mm) REVERT: C 10 ILE cc_start: 0.8523 (mm) cc_final: 0.7983 (tp) REVERT: H 12 VAL cc_start: 0.9224 (p) cc_final: 0.8982 (p) REVERT: H 13 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7240 (tt0) REVERT: J 13 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7457 (tm-30) REVERT: F 11 MET cc_start: 0.8301 (pmm) cc_final: 0.7929 (pmm) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.2102 time to fit residues: 31.6457 Evaluate side-chains 60 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 0.0470 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 108 ASN E 276 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS F 276 GLN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15218 Z= 0.283 Angle : 0.667 7.883 20630 Z= 0.335 Chirality : 0.047 0.195 2320 Planarity : 0.004 0.044 2632 Dihedral : 7.243 67.722 2396 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.36 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.74 (0.20), residues: 1770 helix: -0.74 (0.32), residues: 268 sheet: -0.55 (0.28), residues: 328 loop : -1.50 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 414 HIS 0.006 0.001 HIS F 417 PHE 0.016 0.002 PHE E 89 TYR 0.016 0.001 TYR F 91 ARG 0.004 0.000 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7240 (tt0) REVERT: J 13 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7478 (tm-30) REVERT: F 11 MET cc_start: 0.8406 (pmm) cc_final: 0.7921 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2328 time to fit residues: 31.9771 Evaluate side-chains 59 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 328 GLN ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15218 Z= 0.272 Angle : 0.635 8.183 20630 Z= 0.322 Chirality : 0.046 0.216 2320 Planarity : 0.004 0.045 2632 Dihedral : 7.046 69.033 2396 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.02 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.59 (0.20), residues: 1770 helix: -0.30 (0.32), residues: 268 sheet: -0.59 (0.28), residues: 328 loop : -1.43 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 412 HIS 0.006 0.001 HIS F 21 PHE 0.014 0.001 PHE E 381 TYR 0.013 0.001 TYR F 91 ARG 0.003 0.000 ARG F 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8005 (mm-30) REVERT: H 12 VAL cc_start: 0.9254 (p) cc_final: 0.9042 (p) REVERT: H 13 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7159 (tm-30) REVERT: H 17 LEU cc_start: 0.6663 (mt) cc_final: 0.6450 (mt) REVERT: J 13 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7447 (tm-30) REVERT: F 11 MET cc_start: 0.8454 (pmm) cc_final: 0.7927 (pmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2193 time to fit residues: 29.7761 Evaluate side-chains 56 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 784 GLN C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15218 Z= 0.316 Angle : 0.681 8.796 20630 Z= 0.342 Chirality : 0.047 0.194 2320 Planarity : 0.004 0.044 2632 Dihedral : 7.233 70.150 2396 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.27 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.56 (0.20), residues: 1770 helix: -0.21 (0.32), residues: 268 sheet: -0.64 (0.28), residues: 338 loop : -1.42 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 412 HIS 0.005 0.001 HIS E 829 PHE 0.015 0.002 PHE E 381 TYR 0.015 0.002 TYR E 91 ARG 0.003 0.000 ARG E 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8165 (mm-30) REVERT: H 13 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7275 (tt0) REVERT: H 15 LEU cc_start: 0.9400 (pp) cc_final: 0.9095 (tt) REVERT: J 13 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7449 (tm-30) REVERT: F 11 MET cc_start: 0.8449 (pmm) cc_final: 0.7865 (pmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2197 time to fit residues: 29.3221 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 169 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15218 Z= 0.174 Angle : 0.601 8.970 20630 Z= 0.306 Chirality : 0.046 0.194 2320 Planarity : 0.003 0.042 2632 Dihedral : 6.945 69.369 2396 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.44 (0.21), residues: 1770 helix: -0.14 (0.32), residues: 268 sheet: -0.58 (0.28), residues: 328 loop : -1.31 (0.20), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 559 HIS 0.005 0.001 HIS E 829 PHE 0.013 0.001 PHE F 427 TYR 0.013 0.001 TYR C 14 ARG 0.003 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.735 Fit side-chains REVERT: A 17 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8131 (mm-30) REVERT: H 13 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7341 (tt0) REVERT: J 13 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7483 (tm-30) REVERT: J 17 LEU cc_start: 0.6747 (mt) cc_final: 0.6478 (mt) REVERT: F 11 MET cc_start: 0.8362 (pmm) cc_final: 0.7867 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2270 time to fit residues: 31.2460 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 15 GLN G 18 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15218 Z= 0.225 Angle : 0.628 9.756 20630 Z= 0.317 Chirality : 0.047 0.304 2320 Planarity : 0.003 0.042 2632 Dihedral : 6.875 68.596 2396 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.70 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.34 (0.21), residues: 1770 helix: 0.12 (0.33), residues: 260 sheet: -0.56 (0.28), residues: 328 loop : -1.27 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 414 HIS 0.005 0.001 HIS E 829 PHE 0.012 0.001 PHE E 427 TYR 0.011 0.001 TYR F 849 ARG 0.002 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.588 Fit side-chains REVERT: A 17 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8184 (mm-30) REVERT: H 13 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7349 (tt0) REVERT: J 13 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 11 MET cc_start: 0.8377 (pmm) cc_final: 0.7879 (pmm) REVERT: F 806 MET cc_start: 0.8313 (ptp) cc_final: 0.8033 (mpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2106 time to fit residues: 25.6422 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 142 optimal weight: 0.0270 chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15218 Z= 0.182 Angle : 0.601 10.199 20630 Z= 0.304 Chirality : 0.046 0.263 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.767 66.865 2396 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.46 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1770 helix: -0.03 (0.32), residues: 272 sheet: -0.51 (0.28), residues: 328 loop : -1.27 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 412 HIS 0.004 0.001 HIS E 829 PHE 0.010 0.001 PHE E 705 TYR 0.055 0.001 TYR C 19 ARG 0.002 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.689 Fit side-chains REVERT: A 17 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8172 (mm-30) REVERT: H 13 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7351 (tt0) REVERT: J 13 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7468 (tm-30) REVERT: F 11 MET cc_start: 0.8362 (pmm) cc_final: 0.7880 (pmm) REVERT: F 806 MET cc_start: 0.8264 (ptp) cc_final: 0.8004 (mpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2221 time to fit residues: 29.4220 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 116 optimal weight: 0.0070 chunk 175 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15218 Z= 0.159 Angle : 0.601 10.769 20630 Z= 0.302 Chirality : 0.047 0.477 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.705 66.128 2396 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1770 helix: 0.04 (0.32), residues: 274 sheet: -0.46 (0.28), residues: 328 loop : -1.23 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 412 HIS 0.004 0.001 HIS E 829 PHE 0.009 0.001 PHE E 565 TYR 0.011 0.001 TYR F 849 ARG 0.002 0.000 ARG F 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8134 (mm-30) REVERT: H 13 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7445 (tt0) REVERT: J 13 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7418 (tm-30) REVERT: F 11 MET cc_start: 0.8314 (pmm) cc_final: 0.7853 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2164 time to fit residues: 27.5673 Evaluate side-chains 53 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.089997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060528 restraints weight = 66853.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061197 restraints weight = 39641.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061521 restraints weight = 29485.943| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15218 Z= 0.154 Angle : 0.585 10.652 20630 Z= 0.295 Chirality : 0.046 0.334 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.591 65.939 2396 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.12 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.18 (0.21), residues: 1770 helix: 0.38 (0.33), residues: 262 sheet: -0.48 (0.27), residues: 338 loop : -1.20 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 559 HIS 0.004 0.001 HIS E 829 PHE 0.018 0.001 PHE E 572 TYR 0.015 0.001 TYR C 14 ARG 0.002 0.000 ARG E 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.70 seconds wall clock time: 43 minutes 50.79 seconds (2630.79 seconds total)