Starting phenix.real_space_refine on Thu Jun 12 21:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.map" model { file = "/net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guy_34281/06_2025/8guy_34281.cif" } resolution = 4.18 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= 0.048 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 114 5.16 5 C 9006 2.51 5 N 2456 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14222 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "F" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 residue: pdb=" N ATYR D 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 26 " occ=0.50 Time building chain proxies: 14.68, per 1000 atoms: 1.03 Number of scatterers: 14222 At special positions: 0 Unit cell: (119.84, 132.68, 174.41, 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 114 16.00 O 2646 8.00 N 2456 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 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=2.04 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=2.02 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=2.04 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 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 683 " - pdb=" SG CYS F 683 " distance=2.04 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.02 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.02 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.04 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.04 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=2.04 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 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 32 sheets defined 15.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.923A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.096A pdb=" N ILE E 131 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.034A pdb=" N ILE E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.534A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 3.866A 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 354 through 359 Processing helix chain 'E' and resid 413 through 417 removed outlier: 3.526A pdb=" N HIS E 417 " --> pdb=" O TRP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 444 removed outlier: 3.851A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 644 removed outlier: 3.592A pdb=" N PHE E 642 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 643 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 644 " --> pdb=" O LEU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 714 removed outlier: 3.675A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 712 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 714 " --> pdb=" O HIS E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 813 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.532A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.070A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.531A pdb=" N GLU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 removed outlier: 4.165A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.021A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.509A pdb=" N ASN F 152 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' 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 354 through 359 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.510A pdb=" N HIS F 417 " --> pdb=" O TRP F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.877A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 644 removed outlier: 3.530A pdb=" N PHE F 642 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 644 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 714 removed outlier: 3.642A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 708 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 711 " --> pdb=" O ASP F 707 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 712 " --> pdb=" O TYR F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU E 6 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE E 29 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS E 8 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.832A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU E 36 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE E 13 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET E 38 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 64 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.362A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312 removed outlier: 3.856A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321 removed outlier: 3.884A pdb=" N LYS E 319 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.678A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 599 through 605 removed outlier: 5.491A pdb=" N ASP E 600 " --> pdb=" O LYS E 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 616 " --> pdb=" O ASP E 600 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 612 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 611 " --> pdb=" O ILE E 770 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 4.124A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 819 through 822 removed outlier: 3.543A pdb=" N VAL E 828 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 886 " --> pdb=" O TRP E 897 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP E 897 " --> pdb=" O ILE E 886 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA E 888 " --> pdb=" O GLY E 895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU F 6 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE F 29 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS F 8 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 14 removed outlier: 3.658A pdb=" N PHE F 64 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 37 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.237A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC3, first strand: chain 'F' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.801A pdb=" N ILE F 364 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 318 through 321 removed outlier: 3.777A pdb=" N LYS F 319 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE F 341 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AC9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.530A pdb=" N LYS F 508 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 564 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 599 through 605 removed outlier: 5.430A pdb=" N ASP F 600 " --> pdb=" O LYS F 616 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS F 616 " --> pdb=" O ASP F 600 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 612 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 611 " --> pdb=" O ILE F 770 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 761 through 762 removed outlier: 3.680A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 819 through 822 removed outlier: 3.545A pdb=" N VAL F 828 " --> pdb=" O LEU F 874 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 886 " --> pdb=" O TRP F 897 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP F 897 " --> pdb=" O ILE F 886 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA F 888 " --> pdb=" O GLY F 895 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 789 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: 5.44 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: 4683 1.35 - 1.48: 3636 1.48 - 1.60: 6121 1.60 - 1.73: 0 1.73 - 1.85: 136 Bond restraints: 14576 Sorted by residual: bond pdb=" CB GLU F 637 " pdb=" CG GLU F 637 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB CYS F 435 " pdb=" SG CYS F 435 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB GLU E 637 " pdb=" CG GLU E 637 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB CYS E 435 " pdb=" SG CYS E 435 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CA THR E 578 " pdb=" CB THR E 578 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.61e-02 3.86e+03 2.51e+00 ... (remaining 14571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18992 2.32 - 4.63: 652 4.63 - 6.95: 97 6.95 - 9.27: 23 9.27 - 11.59: 6 Bond angle restraints: 19770 Sorted by residual: angle pdb=" N VAL E 445 " pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 112.96 105.76 7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" C ARG E 577 " pdb=" N THR E 578 " pdb=" CA THR E 578 " ideal model delta sigma weight residual 122.82 128.40 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ARG F 14 " pdb=" N ASN F 15 " pdb=" CA ASN F 15 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLU E 808 " pdb=" CA GLU E 808 " pdb=" C GLU E 808 " ideal model delta sigma weight residual 110.53 115.59 -5.06 1.32e+00 5.74e-01 1.47e+01 angle pdb=" CA CYS F 308 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 19765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7845 17.90 - 35.80: 830 35.80 - 53.70: 130 53.70 - 71.60: 47 71.60 - 89.51: 16 Dihedral angle restraints: 8868 sinusoidal: 3704 harmonic: 5164 Sorted by residual: dihedral pdb=" CA PRO E 243 " pdb=" C PRO E 243 " pdb=" N PRO E 244 " pdb=" CA PRO E 244 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 dihedral pdb=" CB CYS F 647 " pdb=" SG CYS F 647 " pdb=" SG CYS F 860 " pdb=" CB CYS F 860 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA PRO F 243 " pdb=" C PRO F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 134.03 45.97 0 5.00e+00 4.00e-02 8.45e+01 ... (remaining 8865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1654 0.065 - 0.131: 403 0.131 - 0.196: 67 0.196 - 0.262: 15 0.262 - 0.327: 1 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CB THR F 790 " pdb=" CA THR F 790 " pdb=" OG1 THR F 790 " pdb=" CG2 THR F 790 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR F 790 " pdb=" N THR F 790 " pdb=" C THR F 790 " pdb=" CB THR F 790 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE E 781 " pdb=" CA ILE E 781 " pdb=" CG1 ILE E 781 " pdb=" CG2 ILE E 781 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2137 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 243 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO F 244 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 244 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 244 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 242 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO F 243 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " 0.047 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2977 2.78 - 3.31: 12547 3.31 - 3.84: 23562 3.84 - 4.37: 25822 4.37 - 4.90: 43345 Nonbonded interactions: 108253 Sorted by model distance: nonbonded pdb=" OD1 ASP E 59 " pdb=" OG SER E 85 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP F 59 " pdb=" OG SER F 85 " model vdw 2.258 3.040 nonbonded pdb=" OG SER E 116 " pdb=" OD1 ASN E 143 " model vdw 2.299 3.040 nonbonded pdb=" OG SER F 116 " pdb=" OD1 ASN F 143 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR F 334 " pdb=" OE1 GLU F 362 " model vdw 2.333 3.040 ... (remaining 108248 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 3 through 25 or resid 27)) selection = (chain 'D' and (resid 3 through 25 or resid 27)) } ncs_group { reference = (chain 'E' and (resid 1 through 143 or resid 145 through 907)) selection = (chain 'F' and (resid 1 through 143 or resid 145 through 907)) } 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=0.50 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: 11.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.120 Process input model: 42.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.005 0.057 14620 Z= 0.243 Angle : 1.017 11.587 19858 Z= 0.544 Chirality : 0.060 0.327 2140 Planarity : 0.007 0.112 2566 Dihedral : 14.547 89.506 5408 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.12 % 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: -4.23 (0.17), residues: 1744 helix: -4.43 (0.16), residues: 216 sheet: -1.99 (0.27), residues: 316 loop : -2.92 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 412 HIS 0.007 0.001 HIS F 275 PHE 0.021 0.002 PHE E 776 TYR 0.018 0.002 TYR F 708 ARG 0.013 0.001 ARG E 774 Details of bonding type rmsd hydrogen bonds : bond 0.33485 ( 291) hydrogen bonds : angle 10.67611 ( 789) SS BOND : bond 0.00608 ( 44) SS BOND : angle 2.51315 ( 88) covalent geometry : bond 0.00511 (14576) covalent geometry : angle 1.00498 (19770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8459 (tp) cc_final: 0.8086 (tp) REVERT: E 405 ASN cc_start: 0.8688 (m-40) cc_final: 0.8431 (m110) REVERT: E 439 ILE cc_start: 0.9224 (pt) cc_final: 0.8977 (mt) REVERT: E 442 MET cc_start: 0.9351 (tpt) cc_final: 0.8902 (tpt) REVERT: E 698 GLU cc_start: 0.7758 (pp20) cc_final: 0.7524 (tm-30) REVERT: A 2 ILE cc_start: 0.9529 (tt) cc_final: 0.9317 (tt) REVERT: C 17 GLU cc_start: 0.8504 (pp20) cc_final: 0.8073 (pp20) REVERT: F 439 ILE cc_start: 0.8987 (pt) cc_final: 0.8698 (mt) REVERT: F 442 MET cc_start: 0.9295 (tpt) cc_final: 0.9005 (tpt) REVERT: F 698 GLU cc_start: 0.8177 (pp20) cc_final: 0.7891 (tm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2236 time to fit residues: 47.5443 Evaluate side-chains 79 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 GLN E 282 ASN E 589 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 32 HIS F 177 GLN F 249 GLN F 431 ASN F 589 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.091275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061224 restraints weight = 157242.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.062759 restraints weight = 79568.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063345 restraints weight = 47769.581| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14620 Z= 0.151 Angle : 0.708 6.713 19858 Z= 0.371 Chirality : 0.047 0.192 2140 Planarity : 0.006 0.100 2566 Dihedral : 6.546 76.358 1938 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.25 % Allowed : 3.24 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.45 (0.18), residues: 1744 helix: -3.22 (0.26), residues: 190 sheet: -1.80 (0.28), residues: 306 loop : -2.44 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 412 HIS 0.008 0.001 HIS E 858 PHE 0.018 0.002 PHE E 497 TYR 0.013 0.001 TYR E 708 ARG 0.005 0.001 ARG F 717 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 291) hydrogen bonds : angle 7.18524 ( 789) SS BOND : bond 0.00370 ( 44) SS BOND : angle 1.97293 ( 88) covalent geometry : bond 0.00342 (14576) covalent geometry : angle 0.69677 (19770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7984 (tp) cc_final: 0.7062 (tp) REVERT: E 57 ILE cc_start: 0.9046 (mt) cc_final: 0.8697 (mt) REVERT: E 314 LEU cc_start: 0.9484 (tp) cc_final: 0.9261 (tt) REVERT: E 405 ASN cc_start: 0.8943 (m-40) cc_final: 0.8724 (m-40) REVERT: E 442 MET cc_start: 0.9121 (tpt) cc_final: 0.8690 (tpt) REVERT: E 572 PHE cc_start: 0.7444 (t80) cc_final: 0.7201 (t80) REVERT: D 6 LEU cc_start: 0.9239 (mt) cc_final: 0.9000 (mt) REVERT: F 405 ASN cc_start: 0.8479 (m-40) cc_final: 0.8166 (p0) REVERT: F 442 MET cc_start: 0.9052 (tpt) cc_final: 0.8844 (tpt) REVERT: F 707 ASP cc_start: 0.8617 (m-30) cc_final: 0.8335 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2134 time to fit residues: 39.1244 Evaluate side-chains 67 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 160 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 143 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN E 431 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS F 187 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061473 restraints weight = 195798.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062205 restraints weight = 89580.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064309 restraints weight = 51276.299| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14620 Z= 0.154 Angle : 0.672 9.211 19858 Z= 0.348 Chirality : 0.046 0.189 2140 Planarity : 0.005 0.103 2566 Dihedral : 6.202 83.807 1938 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.25 % Allowed : 2.86 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.04 (0.19), residues: 1744 helix: -2.23 (0.32), residues: 190 sheet: -1.68 (0.27), residues: 344 loop : -2.21 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 412 HIS 0.008 0.001 HIS E 429 PHE 0.017 0.002 PHE F 178 TYR 0.015 0.001 TYR F 401 ARG 0.004 0.000 ARG E 794 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 291) hydrogen bonds : angle 6.43783 ( 789) SS BOND : bond 0.00389 ( 44) SS BOND : angle 1.52706 ( 88) covalent geometry : bond 0.00352 (14576) covalent geometry : angle 0.66552 (19770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8081 (tp) cc_final: 0.7263 (tp) REVERT: E 504 MET cc_start: 0.8316 (mtp) cc_final: 0.8015 (mtp) REVERT: C 14 TYR cc_start: 0.7948 (t80) cc_final: 0.7636 (t80) REVERT: D 6 LEU cc_start: 0.9221 (mt) cc_final: 0.9004 (mt) REVERT: F 36 LEU cc_start: 0.8545 (tp) cc_final: 0.8153 (tp) REVERT: F 333 CYS cc_start: 0.6506 (p) cc_final: 0.6239 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2355 time to fit residues: 37.6108 Evaluate side-chains 65 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061933 restraints weight = 210793.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064045 restraints weight = 99089.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065212 restraints weight = 59673.293| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14620 Z= 0.139 Angle : 0.635 6.609 19858 Z= 0.329 Chirality : 0.046 0.189 2140 Planarity : 0.005 0.105 2566 Dihedral : 5.989 82.616 1938 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.25 % Allowed : 1.81 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.82 (0.20), residues: 1744 helix: -1.66 (0.35), residues: 194 sheet: -1.57 (0.27), residues: 350 loop : -2.13 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 529 HIS 0.003 0.000 HIS F 429 PHE 0.022 0.002 PHE E 572 TYR 0.011 0.001 TYR E 401 ARG 0.003 0.000 ARG E 702 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 291) hydrogen bonds : angle 6.15100 ( 789) SS BOND : bond 0.00263 ( 44) SS BOND : angle 1.39043 ( 88) covalent geometry : bond 0.00323 (14576) covalent geometry : angle 0.62916 (19770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8111 (tp) cc_final: 0.7317 (tp) REVERT: E 314 LEU cc_start: 0.9432 (tp) cc_final: 0.9226 (tt) REVERT: E 405 ASN cc_start: 0.8916 (m-40) cc_final: 0.8540 (m110) REVERT: E 442 MET cc_start: 0.9206 (tpt) cc_final: 0.8710 (tpt) REVERT: E 504 MET cc_start: 0.8328 (mtp) cc_final: 0.8076 (mtm) REVERT: D 6 LEU cc_start: 0.9136 (mt) cc_final: 0.8932 (mt) REVERT: F 36 LEU cc_start: 0.8236 (tp) cc_final: 0.7951 (tp) REVERT: F 333 CYS cc_start: 0.6192 (p) cc_final: 0.5951 (p) REVERT: F 405 ASN cc_start: 0.8665 (m-40) cc_final: 0.8405 (m110) REVERT: F 504 MET cc_start: 0.8157 (mtp) cc_final: 0.7902 (mtm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2345 time to fit residues: 32.9698 Evaluate side-chains 65 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 84 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 HIS ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 423 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.090947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062469 restraints weight = 191523.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063977 restraints weight = 92369.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065021 restraints weight = 55078.905| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14620 Z= 0.122 Angle : 0.614 7.052 19858 Z= 0.315 Chirality : 0.045 0.189 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.686 82.008 1938 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.25 % Allowed : 1.68 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.59 (0.20), residues: 1744 helix: -1.36 (0.36), residues: 194 sheet: -1.36 (0.27), residues: 350 loop : -2.01 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 529 HIS 0.003 0.000 HIS D 5 PHE 0.015 0.001 PHE F 178 TYR 0.011 0.001 TYR E 401 ARG 0.007 0.000 ARG F 539 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 291) hydrogen bonds : angle 5.76754 ( 789) SS BOND : bond 0.00322 ( 44) SS BOND : angle 1.50826 ( 88) covalent geometry : bond 0.00285 (14576) covalent geometry : angle 0.60741 (19770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7961 (tp) cc_final: 0.7150 (tp) REVERT: E 294 MET cc_start: 0.8506 (ppp) cc_final: 0.7891 (tpp) REVERT: E 333 CYS cc_start: 0.6588 (p) cc_final: 0.6312 (p) REVERT: E 405 ASN cc_start: 0.9030 (m-40) cc_final: 0.8576 (m110) REVERT: E 504 MET cc_start: 0.8277 (mtp) cc_final: 0.8016 (mtm) REVERT: A 14 TYR cc_start: 0.8110 (t80) cc_final: 0.7528 (t80) REVERT: A 17 GLU cc_start: 0.8663 (pp20) cc_final: 0.8244 (pp20) REVERT: B 6 LEU cc_start: 0.9094 (mt) cc_final: 0.8788 (mp) REVERT: C 14 TYR cc_start: 0.8083 (t80) cc_final: 0.7128 (t80) REVERT: D 6 LEU cc_start: 0.9174 (mt) cc_final: 0.8968 (mt) REVERT: F 36 LEU cc_start: 0.8281 (tp) cc_final: 0.8063 (tp) REVERT: F 333 CYS cc_start: 0.6518 (p) cc_final: 0.6311 (p) REVERT: F 405 ASN cc_start: 0.8932 (m-40) cc_final: 0.8498 (m110) REVERT: F 504 MET cc_start: 0.8321 (mtp) cc_final: 0.7991 (mtm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2419 time to fit residues: 37.4753 Evaluate side-chains 66 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 105 optimal weight: 0.0060 chunk 46 optimal weight: 0.0770 chunk 135 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 HIS ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.091169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061638 restraints weight = 183291.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063640 restraints weight = 87068.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064596 restraints weight = 51803.550| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14620 Z= 0.111 Angle : 0.613 7.134 19858 Z= 0.313 Chirality : 0.045 0.183 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.576 81.304 1938 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.25 % Allowed : 0.93 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.46 (0.20), residues: 1744 helix: -1.29 (0.37), residues: 194 sheet: -1.20 (0.28), residues: 340 loop : -1.93 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 529 HIS 0.003 0.000 HIS E 313 PHE 0.014 0.001 PHE E 497 TYR 0.013 0.001 TYR C 14 ARG 0.008 0.000 ARG F 270 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 291) hydrogen bonds : angle 5.57836 ( 789) SS BOND : bond 0.00245 ( 44) SS BOND : angle 1.33292 ( 88) covalent geometry : bond 0.00257 (14576) covalent geometry : angle 0.60796 (19770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7930 (tp) cc_final: 0.7155 (tp) REVERT: E 87 LEU cc_start: 0.9511 (mp) cc_final: 0.9263 (mp) REVERT: E 294 MET cc_start: 0.8468 (ppp) cc_final: 0.7902 (tpp) REVERT: E 333 CYS cc_start: 0.6666 (p) cc_final: 0.6431 (p) REVERT: E 405 ASN cc_start: 0.8992 (m-40) cc_final: 0.8520 (m110) REVERT: E 442 MET cc_start: 0.9168 (tpt) cc_final: 0.8847 (tpt) REVERT: E 504 MET cc_start: 0.8462 (mtp) cc_final: 0.8141 (mtm) REVERT: A 14 TYR cc_start: 0.8040 (t80) cc_final: 0.7391 (t80) REVERT: A 17 GLU cc_start: 0.8655 (pp20) cc_final: 0.8290 (pp20) REVERT: B 6 LEU cc_start: 0.9178 (mt) cc_final: 0.8868 (mt) REVERT: C 14 TYR cc_start: 0.8189 (t80) cc_final: 0.7898 (t80) REVERT: F 36 LEU cc_start: 0.8219 (tp) cc_final: 0.7993 (tp) REVERT: F 333 CYS cc_start: 0.6613 (p) cc_final: 0.6394 (p) REVERT: F 405 ASN cc_start: 0.8950 (m-40) cc_final: 0.8490 (m110) REVERT: F 442 MET cc_start: 0.9226 (tpt) cc_final: 0.8908 (tpt) REVERT: F 504 MET cc_start: 0.8340 (mtp) cc_final: 0.7999 (mtm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1966 time to fit residues: 29.6955 Evaluate side-chains 65 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 164 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.089675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062506 restraints weight = 221771.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.061410 restraints weight = 102735.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063953 restraints weight = 61353.300| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14620 Z= 0.157 Angle : 0.627 7.209 19858 Z= 0.321 Chirality : 0.046 0.181 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.606 79.966 1938 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.25 % Allowed : 0.87 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.46 (0.20), residues: 1744 helix: -1.15 (0.38), residues: 194 sheet: -1.29 (0.27), residues: 350 loop : -1.93 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 412 HIS 0.005 0.001 HIS E 313 PHE 0.012 0.001 PHE E 497 TYR 0.011 0.001 TYR E 60 ARG 0.006 0.000 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 291) hydrogen bonds : angle 5.59980 ( 789) SS BOND : bond 0.00240 ( 44) SS BOND : angle 1.38952 ( 88) covalent geometry : bond 0.00361 (14576) covalent geometry : angle 0.62198 (19770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7956 (tp) cc_final: 0.7186 (tp) REVERT: E 294 MET cc_start: 0.8527 (ppp) cc_final: 0.7977 (tpp) REVERT: E 333 CYS cc_start: 0.6712 (p) cc_final: 0.6448 (p) REVERT: E 405 ASN cc_start: 0.8951 (m-40) cc_final: 0.8575 (m110) REVERT: E 504 MET cc_start: 0.8335 (mtp) cc_final: 0.8081 (mtm) REVERT: A 14 TYR cc_start: 0.8095 (t80) cc_final: 0.7569 (t80) REVERT: A 17 GLU cc_start: 0.8767 (pp20) cc_final: 0.8463 (pp20) REVERT: B 6 LEU cc_start: 0.9127 (mt) cc_final: 0.8917 (mt) REVERT: C 17 GLU cc_start: 0.8754 (pp20) cc_final: 0.8485 (pp20) REVERT: F 333 CYS cc_start: 0.6665 (p) cc_final: 0.6459 (p) REVERT: F 405 ASN cc_start: 0.8788 (m-40) cc_final: 0.8548 (m110) REVERT: F 442 MET cc_start: 0.9185 (tpt) cc_final: 0.8879 (tpt) REVERT: F 504 MET cc_start: 0.8271 (mtp) cc_final: 0.7979 (mtm) REVERT: F 602 ILE cc_start: 0.9035 (mm) cc_final: 0.8738 (mm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1918 time to fit residues: 27.2809 Evaluate side-chains 63 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS E 527 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060286 restraints weight = 225772.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060849 restraints weight = 112143.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061974 restraints weight = 67600.615| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14620 Z= 0.237 Angle : 0.729 8.602 19858 Z= 0.373 Chirality : 0.048 0.168 2140 Planarity : 0.006 0.108 2566 Dihedral : 6.027 80.019 1938 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.25 % Allowed : 0.62 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.67 (0.20), residues: 1744 helix: -1.41 (0.35), residues: 206 sheet: -1.54 (0.27), residues: 350 loop : -2.02 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 529 HIS 0.007 0.001 HIS F 417 PHE 0.016 0.002 PHE D 24 TYR 0.020 0.002 TYR E 579 ARG 0.007 0.001 ARG F 498 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 291) hydrogen bonds : angle 5.91762 ( 789) SS BOND : bond 0.00357 ( 44) SS BOND : angle 1.51233 ( 88) covalent geometry : bond 0.00543 (14576) covalent geometry : angle 0.72364 (19770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7990 (tp) cc_final: 0.7116 (tp) REVERT: E 333 CYS cc_start: 0.7120 (p) cc_final: 0.6788 (p) REVERT: E 405 ASN cc_start: 0.8990 (m-40) cc_final: 0.8690 (m110) REVERT: E 442 MET cc_start: 0.9308 (tpt) cc_final: 0.8745 (tpt) REVERT: E 504 MET cc_start: 0.8399 (mtp) cc_final: 0.8068 (mtm) REVERT: A 14 TYR cc_start: 0.8319 (t80) cc_final: 0.7936 (t80) REVERT: B 6 LEU cc_start: 0.9062 (mt) cc_final: 0.8836 (mt) REVERT: D 6 LEU cc_start: 0.9244 (mt) cc_final: 0.9043 (mt) REVERT: F 56 MET cc_start: 0.8224 (tpp) cc_final: 0.7873 (tpt) REVERT: F 256 PHE cc_start: 0.9342 (p90) cc_final: 0.9122 (p90) REVERT: F 442 MET cc_start: 0.9274 (tpt) cc_final: 0.8949 (tpt) REVERT: F 504 MET cc_start: 0.8256 (mtp) cc_final: 0.7999 (mtm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2724 time to fit residues: 31.6844 Evaluate side-chains 54 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 11 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.088770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058145 restraints weight = 187717.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060562 restraints weight = 87967.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061567 restraints weight = 48093.348| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14620 Z= 0.139 Angle : 0.632 7.273 19858 Z= 0.323 Chirality : 0.046 0.173 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.711 80.548 1938 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.25 % Allowed : 0.50 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.41 (0.20), residues: 1744 helix: -1.10 (0.38), residues: 194 sheet: -1.32 (0.29), residues: 314 loop : -1.88 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 529 HIS 0.003 0.001 HIS F 263 PHE 0.015 0.001 PHE E 497 TYR 0.015 0.001 TYR C 14 ARG 0.004 0.000 ARG F 804 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 291) hydrogen bonds : angle 5.67236 ( 789) SS BOND : bond 0.00276 ( 44) SS BOND : angle 1.42114 ( 88) covalent geometry : bond 0.00324 (14576) covalent geometry : angle 0.62637 (19770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7857 (tp) cc_final: 0.6956 (tp) REVERT: E 294 MET cc_start: 0.8452 (ppp) cc_final: 0.7866 (tpp) REVERT: E 333 CYS cc_start: 0.6903 (p) cc_final: 0.6660 (p) REVERT: E 405 ASN cc_start: 0.9022 (m-40) cc_final: 0.8611 (m110) REVERT: E 442 MET cc_start: 0.9257 (tpt) cc_final: 0.8750 (tpt) REVERT: E 504 MET cc_start: 0.8490 (mtp) cc_final: 0.8165 (mtm) REVERT: B 6 LEU cc_start: 0.9168 (mt) cc_final: 0.8868 (mt) REVERT: F 256 PHE cc_start: 0.9328 (p90) cc_final: 0.9122 (p90) REVERT: F 405 ASN cc_start: 0.8838 (m-40) cc_final: 0.8444 (m110) REVERT: F 442 MET cc_start: 0.9244 (tpt) cc_final: 0.8950 (tpt) REVERT: F 504 MET cc_start: 0.8461 (mtp) cc_final: 0.8163 (mtm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2563 time to fit residues: 32.4402 Evaluate side-chains 57 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.091185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064415 restraints weight = 207295.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064931 restraints weight = 98823.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065840 restraints weight = 59712.863| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14620 Z= 0.097 Angle : 0.603 7.774 19858 Z= 0.304 Chirality : 0.045 0.178 2140 Planarity : 0.005 0.111 2566 Dihedral : 5.337 79.387 1938 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.25 % Allowed : 0.00 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.22 (0.20), residues: 1744 helix: -1.13 (0.37), residues: 200 sheet: -1.15 (0.29), residues: 334 loop : -1.72 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 529 HIS 0.003 0.001 HIS E 263 PHE 0.015 0.001 PHE E 497 TYR 0.009 0.001 TYR E 60 ARG 0.004 0.000 ARG E 702 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 291) hydrogen bonds : angle 5.39955 ( 789) SS BOND : bond 0.00272 ( 44) SS BOND : angle 1.19484 ( 88) covalent geometry : bond 0.00223 (14576) covalent geometry : angle 0.59859 (19770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7770 (tp) cc_final: 0.6920 (tp) REVERT: E 262 LEU cc_start: 0.9227 (mp) cc_final: 0.9006 (mm) REVERT: E 294 MET cc_start: 0.8401 (ppp) cc_final: 0.7873 (tpp) REVERT: E 333 CYS cc_start: 0.6886 (p) cc_final: 0.6595 (p) REVERT: E 442 MET cc_start: 0.9213 (tpt) cc_final: 0.8912 (tpt) REVERT: E 497 PHE cc_start: 0.8728 (p90) cc_final: 0.8448 (p90) REVERT: E 504 MET cc_start: 0.8361 (mtp) cc_final: 0.8035 (mtm) REVERT: B 6 LEU cc_start: 0.9024 (mt) cc_final: 0.8708 (mt) REVERT: F 256 PHE cc_start: 0.9257 (p90) cc_final: 0.9056 (p90) REVERT: F 333 CYS cc_start: 0.6535 (p) cc_final: 0.6172 (p) REVERT: F 405 ASN cc_start: 0.8750 (m-40) cc_final: 0.8243 (m110) REVERT: F 442 MET cc_start: 0.9259 (tpt) cc_final: 0.8981 (tpt) REVERT: F 504 MET cc_start: 0.8232 (mtp) cc_final: 0.7928 (mtm) REVERT: F 832 TRP cc_start: 0.5983 (p90) cc_final: 0.5726 (p-90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2047 time to fit residues: 30.5747 Evaluate side-chains 67 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 0.0060 chunk 127 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 122 optimal weight: 0.0570 chunk 95 optimal weight: 0.0170 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.091326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063996 restraints weight = 200946.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064397 restraints weight = 101214.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066094 restraints weight = 60310.288| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14620 Z= 0.095 Angle : 0.584 7.623 19858 Z= 0.295 Chirality : 0.045 0.178 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.171 77.244 1938 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.25 % Allowed : 0.12 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.15 (0.20), residues: 1744 helix: -0.88 (0.38), residues: 188 sheet: -1.19 (0.28), residues: 354 loop : -1.68 (0.19), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 529 HIS 0.006 0.000 HIS E 247 PHE 0.015 0.001 PHE E 497 TYR 0.023 0.001 TYR A 14 ARG 0.003 0.000 ARG E 702 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 291) hydrogen bonds : angle 5.32503 ( 789) SS BOND : bond 0.00201 ( 44) SS BOND : angle 1.10078 ( 88) covalent geometry : bond 0.00221 (14576) covalent geometry : angle 0.58091 (19770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.36 seconds wall clock time: 101 minutes 59.06 seconds (6119.06 seconds total)