Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 07:10:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9g_31031/04_2023/7e9g_31031_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 121 5.16 5 Cl 1 4.86 5 C 11960 2.51 5 N 3258 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 71": "NH1" <-> "NH2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R ARG 255": "NH1" <-> "NH2" Residue "R ARG 264": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "R ARG 352": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 416": "NH1" <-> "NH2" Residue "R ARG 433": "NH1" <-> "NH2" Residue "R ARG 442": "NH1" <-> "NH2" Residue "R ARG 750": "NH1" <-> "NH2" Residue "R ARG 788": "NH1" <-> "NH2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S ARG 107": "NH1" <-> "NH2" Residue "S GLU 213": "OE1" <-> "OE2" Residue "S ARG 271": "NH1" <-> "NH2" Residue "S ARG 284": "NH1" <-> "NH2" Residue "S GLU 318": "OE1" <-> "OE2" Residue "S ARG 346": "NH1" <-> "NH2" Residue "S GLU 347": "OE1" <-> "OE2" Residue "S ARG 352": "NH1" <-> "NH2" Residue "S ARG 750": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18816 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 5686 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 37, 'TRANS': 731} Chain breaks: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "S" Number of atoms: 5584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5584 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 36, 'TRANS': 718} Chain breaks: 2 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 201 Chain: "A" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1641 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2213 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 218 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1672 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 875 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'40F': 1, 'HZR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 10.49, per 1000 atoms: 0.56 Number of scatterers: 18816 At special positions: 0 Unit cell: (225.72, 148.39, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 121 16.00 O 3476 8.00 N 3258 7.00 C 11960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 234 " - pdb=" SG CYS R 518 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 362 " distance=2.03 Simple disulfide: pdb=" SG CYS R 400 " - pdb=" SG CYS R 407 " distance=2.03 Simple disulfide: pdb=" SG CYS R 500 " - pdb=" SG CYS R 519 " distance=2.03 Simple disulfide: pdb=" SG CYS R 504 " - pdb=" SG CYS R 522 " distance=2.03 Simple disulfide: pdb=" SG CYS R 525 " - pdb=" SG CYS R 537 " distance=2.03 Simple disulfide: pdb=" SG CYS R 540 " - pdb=" SG CYS R 553 " distance=2.03 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 721 " distance=2.03 Simple disulfide: pdb=" SG CYS S 50 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 234 " - pdb=" SG CYS S 518 " distance=2.03 Simple disulfide: pdb=" SG CYS S 355 " - pdb=" SG CYS S 362 " distance=2.03 Simple disulfide: pdb=" SG CYS S 400 " - pdb=" SG CYS S 407 " distance=2.03 Simple disulfide: pdb=" SG CYS S 500 " - pdb=" SG CYS S 519 " distance=2.03 Simple disulfide: pdb=" SG CYS S 504 " - pdb=" SG CYS S 522 " distance=2.03 Simple disulfide: pdb=" SG CYS S 525 " - pdb=" SG CYS S 537 " distance=2.03 Simple disulfide: pdb=" SG CYS S 540 " - pdb=" SG CYS S 553 " distance=2.03 Simple disulfide: pdb=" SG CYS S 632 " - pdb=" SG CYS S 721 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.70 Conformation dependent library (CDL) restraints added in 3.4 seconds 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 28 sheets defined 29.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'R' and resid 58 through 73 Processing helix chain 'R' and resid 95 through 106 Processing helix chain 'R' and resid 145 through 156 Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 190 through 201 Processing helix chain 'R' and resid 217 through 229 Processing helix chain 'R' and resid 247 through 258 Processing helix chain 'R' and resid 272 through 284 Processing helix chain 'R' and resid 327 through 332 Processing helix chain 'R' and resid 343 through 352 Processing helix chain 'R' and resid 378 through 399 Processing helix chain 'R' and resid 408 through 411 No H-bonds generated for 'chain 'R' and resid 408 through 411' Processing helix chain 'R' and resid 415 through 424 removed outlier: 3.808A pdb=" N LEU R 424 " --> pdb=" O LYS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 591 Processing helix chain 'R' and resid 596 through 600 Processing helix chain 'R' and resid 603 through 623 Processing helix chain 'R' and resid 629 through 663 removed outlier: 4.017A pdb=" N GLY R 640 " --> pdb=" O ARG R 636 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS R 646 " --> pdb=" O ALA R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 676 through 698 Processing helix chain 'R' and resid 726 through 752 removed outlier: 3.798A pdb=" N CYS R 752 " --> pdb=" O LYS R 748 " (cutoff:3.500A) Processing helix chain 'R' and resid 757 through 783 Proline residue: R 778 - end of helix Processing helix chain 'R' and resid 787 through 815 removed outlier: 4.305A pdb=" N THR R 792 " --> pdb=" O ARG R 788 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS R 795 " --> pdb=" O THR R 791 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL R 796 " --> pdb=" O THR R 792 " (cutoff:3.500A) Proline residue: R 812 - end of helix Processing helix chain 'S' and resid 59 through 74 removed outlier: 3.601A pdb=" N GLU S 63 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG S 74 " --> pdb=" O ASP S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 107 Processing helix chain 'S' and resid 146 through 158 Processing helix chain 'S' and resid 170 through 173 Processing helix chain 'S' and resid 188 through 201 Processing helix chain 'S' and resid 215 through 230 removed outlier: 3.542A pdb=" N ARG S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA S 230 " --> pdb=" O LEU S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 247 through 258 Processing helix chain 'S' and resid 272 through 283 Processing helix chain 'S' and resid 325 through 332 Processing helix chain 'S' and resid 345 through 352 removed outlier: 3.592A pdb=" N GLN S 351 " --> pdb=" O GLU S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 399 removed outlier: 3.826A pdb=" N HIS S 390 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 415 through 424 Processing helix chain 'S' and resid 569 through 591 Processing helix chain 'S' and resid 603 through 623 removed outlier: 3.577A pdb=" N TYR S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) Processing helix chain 'S' and resid 629 through 656 removed outlier: 3.858A pdb=" N GLY S 640 " --> pdb=" O ARG S 636 " (cutoff:3.500A) Processing helix chain 'S' and resid 676 through 701 removed outlier: 3.516A pdb=" N GLU S 701 " --> pdb=" O TRP S 697 " (cutoff:3.500A) Processing helix chain 'S' and resid 727 through 748 removed outlier: 3.714A pdb=" N SER S 731 " --> pdb=" O SER S 727 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU S 738 " --> pdb=" O TYR S 734 " (cutoff:3.500A) Processing helix chain 'S' and resid 754 through 782 removed outlier: 5.692A pdb=" N ALA S 759 " --> pdb=" O ASN S 755 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS S 760 " --> pdb=" O PHE S 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE S 761 " --> pdb=" O ASN S 757 " (cutoff:3.500A) Proline residue: S 778 - end of helix Processing helix chain 'S' and resid 788 through 808 Processing helix chain 'S' and resid 811 through 816 Processing helix chain 'A' and resid 10 through 31 Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'R' and resid 35 through 38 removed outlier: 6.364A pdb=" N HIS R 87 " --> pdb=" O GLY R 36 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE R 38 " --> pdb=" O HIS R 87 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU R 89 " --> pdb=" O PHE R 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'R' and resid 208 through 211 removed outlier: 7.016A pdb=" N THR R 290 " --> pdb=" O ALA R 266 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU R 268 " --> pdb=" O THR R 290 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL R 292 " --> pdb=" O LEU R 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 315 through 319 removed outlier: 3.598A pdb=" N GLY R 472 " --> pdb=" O ILE R 455 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR R 457 " --> pdb=" O LYS R 470 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS R 470 " --> pdb=" O THR R 457 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU R 459 " --> pdb=" O TYR R 468 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR R 468 " --> pdb=" O LEU R 459 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 427 through 429 removed outlier: 3.708A pdb=" N PHE R 428 " --> pdb=" O VAL R 441 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 510 through 513 Processing sheet with id= F, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.658A pdb=" N ALA S 86 " --> pdb=" O LEU S 28 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 266 through 269 removed outlier: 7.158A pdb=" N SER S 208 " --> pdb=" O VAL S 267 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N PHE S 269 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL S 210 " --> pdb=" O PHE S 269 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 314 through 319 removed outlier: 3.840A pdb=" N GLY S 472 " --> pdb=" O ILE S 455 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR S 457 " --> pdb=" O LYS S 470 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS S 470 " --> pdb=" O THR S 457 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 510 through 512 removed outlier: 3.649A pdb=" N ILE S 523 " --> pdb=" O LYS S 510 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.834A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.222A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.867A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.087A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.621A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.751A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.622A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.629A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.741A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 12 " --> pdb=" O THR D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.611A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= U, first strand: chain 'D' and resid 69 through 73 removed outlier: 4.227A pdb=" N THR D 69 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.704A pdb=" N LYS D 244 " --> pdb=" O VAL D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 155 through 159 Processing sheet with id= X, first strand: chain 'D' and resid 174 through 179 removed outlier: 3.934A pdb=" N VAL D 226 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.537A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 92 through 98 removed outlier: 4.109A pdb=" N THR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.916A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 72 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 68 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 57 through 59 removed outlier: 3.516A pdb=" N VAL F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N MET F 34 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP F 98 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET F 34 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS F 96 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP F 36 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR F 94 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG F 38 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 92 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1923 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: 6.06 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3044 1.31 - 1.44: 5409 1.44 - 1.56: 10631 1.56 - 1.69: 4 1.69 - 1.82: 159 Bond restraints: 19247 Sorted by residual: bond pdb=" C18 HZR R 902 " pdb=" C19 HZR R 902 " ideal model delta sigma weight residual 1.353 1.525 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C6 40F R 901 " pdb=" C7 40F R 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C6 40F S 901 " pdb=" C7 40F S 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C 40F S 901 " pdb=" C1 40F S 901 " ideal model delta sigma weight residual 1.554 1.414 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C 40F R 901 " pdb=" C1 40F R 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19242 not shown) Histogram of bond angle deviations from ideal: 59.68 - 78.02: 6 78.02 - 96.37: 0 96.37 - 114.72: 11844 114.72 - 133.07: 14364 133.07 - 151.41: 47 Bond angle restraints: 26261 Sorted by residual: angle pdb=" C3 40F S 901 " pdb=" C5 40F S 901 " pdb=" C6 40F S 901 " ideal model delta sigma weight residual 116.92 151.41 -34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C3 40F R 901 " pdb=" C5 40F R 901 " pdb=" C6 40F R 901 " ideal model delta sigma weight residual 116.92 151.20 -34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1 40F S 901 " pdb=" C2 40F S 901 " pdb=" C3 40F S 901 " ideal model delta sigma weight residual 118.97 130.70 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C1 40F R 901 " pdb=" C2 40F R 901 " pdb=" C3 40F R 901 " ideal model delta sigma weight residual 118.97 130.33 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C05 HZR R 902 " pdb=" N06 HZR R 902 " pdb=" C17 HZR R 902 " ideal model delta sigma weight residual 115.44 126.11 -10.67 3.00e+00 1.11e-01 1.26e+01 ... (remaining 26256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 10927 26.29 - 52.59: 320 52.59 - 78.88: 22 78.88 - 105.18: 5 105.18 - 131.47: 2 Dihedral angle restraints: 11276 sinusoidal: 3908 harmonic: 7368 Sorted by residual: dihedral pdb=" CB CYS R 50 " pdb=" SG CYS R 50 " pdb=" SG CYS R 92 " pdb=" CB CYS R 92 " ideal model delta sinusoidal sigma weight residual 93.00 6.35 86.65 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS R 525 " pdb=" SG CYS R 525 " pdb=" SG CYS R 537 " pdb=" CB CYS R 537 " ideal model delta sinusoidal sigma weight residual 93.00 167.36 -74.36 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS R 400 " pdb=" SG CYS R 400 " pdb=" SG CYS R 407 " pdb=" CB CYS R 407 " ideal model delta sinusoidal sigma weight residual 93.00 166.05 -73.05 1 1.00e+01 1.00e-02 6.80e+01 ... (remaining 11273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 3016 0.988 - 1.975: 2 1.975 - 2.963: 0 2.963 - 3.951: 0 3.951 - 4.938: 1 Chirality restraints: 3019 Sorted by residual: chirality pdb=" C09 HZR R 902 " pdb=" C08 HZR R 902 " pdb=" C10 HZR R 902 " pdb=" C16 HZR R 902 " both_signs ideal model delta sigma weight residual False 2.48 -2.46 4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C5 40F S 901 " pdb=" C2 40F S 901 " pdb=" C3 40F S 901 " pdb=" C6 40F S 901 " both_signs ideal model delta sigma weight residual True 2.64 1.34 1.29 2.00e-01 2.50e+01 4.18e+01 chirality pdb=" C5 40F R 901 " pdb=" C2 40F R 901 " pdb=" C3 40F R 901 " pdb=" C6 40F R 901 " both_signs ideal model delta sigma weight residual True 2.64 1.35 1.29 2.00e-01 2.50e+01 4.14e+01 ... (remaining 3016 not shown) Planarity restraints: 3379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 570 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO R 571 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 571 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 571 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY S 570 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO S 571 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO S 571 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO S 571 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 741 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C LEU S 741 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU S 741 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS S 742 " 0.008 2.00e-02 2.50e+03 ... (remaining 3376 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1302 2.74 - 3.28: 19303 3.28 - 3.82: 32052 3.82 - 4.36: 36818 4.36 - 4.90: 63430 Nonbonded interactions: 152905 Sorted by model distance: nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.196 2.440 nonbonded pdb=" OG SER R 262 " pdb=" O ARG R 499 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.270 2.440 nonbonded pdb=" OG SER S 356 " pdb=" OE1 GLN S 359 " model vdw 2.283 2.440 nonbonded pdb=" OE1 GLU S 308 " pdb=" OH TYR S 458 " model vdw 2.299 2.440 ... (remaining 152900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 2 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 29 or (resid 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 85 or (re \ sid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 118)) selection = (chain 'F' and (resid 2 through 10 or (resid 11 through 12 and (name N or name C \ A or name C or name O or name CB )) or resid 13 through 45 or (resid 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 118)) } ncs_group { reference = (chain 'R' and (resid 23 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 353 or (resid 354 and (name N or n \ ame CA or name C or name O or name CB )) or resid 355 through 359 or (resid 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 through 40 \ 1 or (resid 402 and (name N or name CA or name C or name O or name CB )) or resi \ d 403 through 423 or (resid 424 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 or (resid 427 and (name N or name CA or name C \ or name O or name CB )) or resid 428 through 506 or (resid 507 through 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 554 or \ (resid 555 through 556 and (name N or name CA or name C or name O or name CB )) \ or resid 557 through 589 or (resid 590 through 591 and (name N or name CA or na \ me C or name O or name CB )) or resid 592 or (resid 593 through 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 or (re \ sid 599 through 601 and (name N or name CA or name C or name O or name CB )) or \ resid 602 through 613 or (resid 614 through 615 and (name N or name CA or name C \ or name O or name CB )) or resid 616 or (resid 617 and (name N or name CA or na \ me C or name O or name CB )) or resid 618 through 620 or (resid 621 and (name N \ or name CA or name C or name O or name CB )) or resid 622 through 635 or (resid \ 636 through 637 and (name N or name CA or name C or name O or name CB )) or resi \ d 638 through 646 or (resid 647 through 649 and (name N or name CA or name C or \ name O or name CB )) or resid 650 through 652 or (resid 653 and (name N or name \ CA or name C or name O or name CB )) or resid 654 or (resid 655 through 656 and \ (name N or name CA or name C or name O or name CB )) or resid 657 or resid 675 t \ hrough 681 or (resid 682 through 683 and (name N or name CA or name C or name O \ or name CB )) or resid 684 through 686 or (resid 687 and (name N or name CA or n \ ame C or name O or name CB )) or resid 688 through 704 or (resid 705 and (name N \ or name CA or name C or name O or name CB )) or resid 706 or (resid 707 through \ 710 and (name N or name CA or name C or name O or name CB )) or resid 711 throu \ gh 733 or (resid 734 and (name N or name CA or name C or name O or name CB )) or \ resid 735 through 780 or (resid 781 and (name N or name CA or name C or name O \ or name CB )) or resid 782 through 804 or (resid 805 and (name N or name CA or n \ ame C or name O or name CB )) or resid 806 through 816)) selection = (chain 'S' and (resid 23 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 110 or resid 136 through 300 or (r \ esid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 t \ hrough 307 or (resid 308 and (name N or name CA or name C or name O or name CB ) \ ) or resid 309 through 317 or (resid 318 and (name N or name CA or name C or nam \ e O or name CB )) or resid 319 through 334 or (resid 335 and (name N or name CA \ or name C or name O or name CB )) or resid 336 through 500 or (resid 501 through \ 502 and (name N or name CA or name C or name O or name CB )) or resid 503 throu \ gh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) or \ resid 527 through 529 or (resid 530 through 536 and (name N or name CA or name \ C or name O or name CB )) or resid 537 through 541 or (resid 542 and (name N or \ name CA or name C or name O or name CB )) or resid 543 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 through 5 \ 59 or (resid 560 through 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 or (resid 565 through 566 and (name N or name CA or name C or \ name O or name CB )) or resid 567 through 575 or (resid 576 and (name N or name \ CA or name C or name O or name CB )) or resid 577 through 582 or (resid 583 thr \ ough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 o \ r (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 87 through 619 or (resid 620 through 621 and (name N or name CA or name C or nam \ e O or name CB )) or resid 622 through 632 or (resid 633 and (name N or name CA \ or name C or name O or name CB )) or resid 634 through 640 or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 647 or (resid 648 through 649 and (name N or name CA or name C or name O or n \ ame CB )) or resid 650 through 715 or (resid 716 and (name N or name CA or name \ C or name O or name CB )) or resid 717 through 722 or (resid 723 through 726 and \ (name N or name CA or name C or name O or name CB )) or resid 727 through 751 o \ r (resid 752 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 53 through 754 or (resid 755 and (name N or name CA or name C or name O or name \ CB )) or resid 756 through 759 or (resid 760 through 762 and (name N or name CA \ or name C or name O or name CB )) or resid 763 through 765 or (resid 766 and (na \ me N or name CA or name C or name O or name CB )) or resid 767 through 785 or (r \ esid 786 through 787 and (name N or name CA or name C or name O or name CB )) or \ resid 788 through 789 or (resid 790 and (name N or name CA or name C or name O \ or name CB )) or resid 791 through 809 or (resid 810 through 811 and (name N or \ name CA or name C or name O or name CB )) or resid 812 or (resid 813 through 814 \ and (name N or name CA or name C or name O or name CB )) or resid 815 through 8 \ 16)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 14.040 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 50.670 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 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 : 0.004 0.172 19247 Z= 0.271 Angle : 0.586 34.494 26261 Z= 0.291 Chirality : 0.104 4.938 3019 Planarity : 0.003 0.046 3379 Dihedral : 11.661 131.471 6477 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.17 (0.14), residues: 2531 helix: -0.49 (0.16), residues: 820 sheet: -2.65 (0.21), residues: 443 loop : -3.07 (0.14), residues: 1268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.3669 time to fit residues: 179.4241 Evaluate side-chains 237 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 0.0040 chunk 147 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 73 ASN R 191 GLN R 365 HIS R 438 HIS R 469 GLN S 41 HIS S 73 ASN S 97 HIS S 101 GLN S 191 GLN S 365 HIS S 374 GLN S 469 GLN S 592 HIS S 679 GLN S 690 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 62 HIS B 91 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 GLN B 176 GLN B 259 GLN D 142 GLN E 6 GLN E 13 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 19247 Z= 0.157 Angle : 0.480 7.238 26261 Z= 0.245 Chirality : 0.039 0.158 3019 Planarity : 0.004 0.046 3379 Dihedral : 4.426 107.481 2770 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2531 helix: 0.49 (0.17), residues: 833 sheet: -2.22 (0.22), residues: 462 loop : -2.60 (0.15), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 2.141 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 262 average time/residue: 0.3167 time to fit residues: 127.4427 Evaluate side-chains 241 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1739 time to fit residues: 9.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 204 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 HIS R 97 HIS ** R 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS D 142 GLN E 39 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 104 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 19247 Z= 0.512 Angle : 0.722 8.342 26261 Z= 0.375 Chirality : 0.048 0.233 3019 Planarity : 0.005 0.063 3379 Dihedral : 5.909 126.545 2770 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 2531 helix: -0.22 (0.17), residues: 839 sheet: -2.00 (0.22), residues: 481 loop : -2.44 (0.16), residues: 1211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 256 time to evaluate : 2.320 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 34 residues processed: 304 average time/residue: 0.3347 time to fit residues: 155.8037 Evaluate side-chains 262 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1754 time to fit residues: 14.1644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 40.0000 chunk 172 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 359 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN E 73 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19247 Z= 0.215 Angle : 0.536 9.270 26261 Z= 0.277 Chirality : 0.040 0.142 3019 Planarity : 0.004 0.047 3379 Dihedral : 5.333 122.864 2770 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2531 helix: 0.25 (0.17), residues: 835 sheet: -1.81 (0.22), residues: 511 loop : -2.21 (0.17), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 2.304 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 273 average time/residue: 0.3211 time to fit residues: 135.4876 Evaluate side-chains 257 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1811 time to fit residues: 12.3874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 394 ASN S 162 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 3 GLN E 39 GLN E 73 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 19247 Z= 0.440 Angle : 0.677 10.539 26261 Z= 0.349 Chirality : 0.046 0.187 3019 Planarity : 0.005 0.065 3379 Dihedral : 5.968 130.039 2770 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2531 helix: -0.09 (0.17), residues: 838 sheet: -1.83 (0.22), residues: 505 loop : -2.12 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 238 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 282 average time/residue: 0.3126 time to fit residues: 136.7754 Evaluate side-chains 249 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1822 time to fit residues: 11.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 20 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 268 ASN B 340 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19247 Z= 0.208 Angle : 0.557 11.662 26261 Z= 0.283 Chirality : 0.041 0.152 3019 Planarity : 0.004 0.056 3379 Dihedral : 5.303 119.111 2770 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2531 helix: 0.25 (0.18), residues: 846 sheet: -1.69 (0.22), residues: 517 loop : -2.02 (0.17), residues: 1168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 258 average time/residue: 0.3543 time to fit residues: 139.7472 Evaluate side-chains 254 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 237 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1886 time to fit residues: 9.2068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.0010 chunk 136 optimal weight: 0.6980 chunk 242 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 338 ASN S 755 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19247 Z= 0.207 Angle : 0.555 11.425 26261 Z= 0.281 Chirality : 0.040 0.179 3019 Planarity : 0.004 0.049 3379 Dihedral : 5.169 115.406 2770 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2531 helix: 0.49 (0.18), residues: 837 sheet: -1.64 (0.22), residues: 502 loop : -1.92 (0.17), residues: 1192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 258 average time/residue: 0.3389 time to fit residues: 132.4544 Evaluate side-chains 242 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1843 time to fit residues: 7.5020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 120 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 40.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19247 Z= 0.206 Angle : 0.555 10.644 26261 Z= 0.282 Chirality : 0.041 0.183 3019 Planarity : 0.004 0.050 3379 Dihedral : 5.158 115.314 2770 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2531 helix: 0.58 (0.18), residues: 840 sheet: -1.63 (0.22), residues: 512 loop : -1.86 (0.18), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 249 average time/residue: 0.3326 time to fit residues: 126.0281 Evaluate side-chains 241 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1833 time to fit residues: 8.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 226 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 162 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 19247 Z= 0.306 Angle : 0.613 10.431 26261 Z= 0.313 Chirality : 0.043 0.248 3019 Planarity : 0.004 0.047 3379 Dihedral : 5.538 119.671 2770 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2531 helix: 0.41 (0.18), residues: 842 sheet: -1.62 (0.22), residues: 507 loop : -1.84 (0.18), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 246 average time/residue: 0.3261 time to fit residues: 123.6850 Evaluate side-chains 229 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1741 time to fit residues: 4.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19247 Z= 0.241 Angle : 0.581 10.359 26261 Z= 0.297 Chirality : 0.041 0.187 3019 Planarity : 0.004 0.083 3379 Dihedral : 5.440 117.400 2770 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2531 helix: 0.47 (0.18), residues: 840 sheet: -1.61 (0.22), residues: 513 loop : -1.81 (0.18), residues: 1178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 2.142 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 226 average time/residue: 0.3454 time to fit residues: 120.5145 Evaluate side-chains 226 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1912 time to fit residues: 5.8917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** 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 = 0.3980 r_free = 0.3980 target = 0.114198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100799 restraints weight = 43992.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.100153 restraints weight = 41378.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100978 restraints weight = 38374.112| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19247 Z= 0.240 Angle : 0.588 10.188 26261 Z= 0.299 Chirality : 0.041 0.184 3019 Planarity : 0.004 0.083 3379 Dihedral : 5.400 112.439 2770 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2531 helix: 0.50 (0.18), residues: 838 sheet: -1.53 (0.22), residues: 500 loop : -1.79 (0.18), residues: 1193 =============================================================================== Job complete usr+sys time: 3677.29 seconds wall clock time: 67 minutes 58.83 seconds (4078.83 seconds total)