Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 17:01:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/04_2023/8eyy_28724_neut.pdb" } resolution = 4.9 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= 0.003 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 6340 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 9083 2.51 5 N 2446 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14301 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6284 Classifications: {'peptide': 775} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 732} Chain breaks: 6 Chain: "B" Number of atoms: 6540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6540 Classifications: {'peptide': 810} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 764} Chain breaks: 5 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Time building chain proxies: 7.15, per 1000 atoms: 0.50 Number of scatterers: 14301 At special positions: 0 Unit cell: (141.48, 140.4, 178.2, 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 2658 8.00 N 2446 7.00 C 9083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " 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: 5.50 Conformation dependent library (CDL) restraints added in 2.1 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 34 sheets defined 17.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.583A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.120A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.885A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.562A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.936A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.573A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 691 through 716 removed outlier: 3.746A pdb=" N TYR A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.592A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.687A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.713A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.853A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.579A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.918A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.037A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.805A pdb=" N ASP B 814 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.769A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.573A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 Processing helix chain 'F' and resid 71 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.652A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 11 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.652A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 11 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 98 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER A 116 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.554A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.507A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.194A pdb=" N GLU A 471 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 479 Processing sheet with id=AB2, first strand: chain 'A' and resid 500 through 509 removed outlier: 5.793A pdb=" N LEU A 571 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A 503 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A 569 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU A 505 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 567 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 507 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 565 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A 509 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLN A 563 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 601 through 607 removed outlier: 6.566A pdb=" N LYS A 616 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 605 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 614 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 761 through 764 removed outlier: 6.598A pdb=" N ARG A 796 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 764 removed outlier: 3.568A pdb=" N ALA A 805 " --> pdb=" O TYR A 781 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 824 removed outlier: 4.637A pdb=" N GLN A 835 " --> pdb=" O PRO A 819 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 864 removed outlier: 5.456A pdb=" N VAL A 888 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP A 899 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA A 890 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 14 removed outlier: 5.918A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET B 98 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU B 97 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.491A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.793A pdb=" N ILE B 364 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.517A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.343A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 607 removed outlier: 5.414A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.938A pdb=" N GLY B 780 " --> pdb=" O GLN B 637 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 817 through 824 removed outlier: 4.416A pdb=" N GLN B 835 " --> pdb=" O PRO B 819 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 859 through 864 394 hydrogen bonds defined for protein. 1011 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: 5.01 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4673 1.34 - 1.46: 2939 1.46 - 1.58: 6894 1.58 - 1.70: 1 1.70 - 1.81: 138 Bond restraints: 14645 Sorted by residual: bond pdb=" CB PRO B 548 " pdb=" CG PRO B 548 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.15e+00 bond pdb=" CA TYR A 144 " pdb=" C TYR A 144 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.21e-02 6.83e+03 1.77e+00 bond pdb=" C TYR A 144 " pdb=" O TYR A 144 " ideal model delta sigma weight residual 1.234 1.221 0.013 1.14e-02 7.69e+03 1.22e+00 bond pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.56e-02 4.11e+03 1.18e+00 bond pdb=" C ASP A 602 " pdb=" O ASP A 602 " ideal model delta sigma weight residual 1.235 1.240 -0.005 4.70e-03 4.53e+04 1.15e+00 ... (remaining 14640 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 469 106.91 - 113.69: 7927 113.69 - 120.46: 5384 120.46 - 127.23: 5881 127.23 - 134.01: 183 Bond angle restraints: 19844 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N PRO B 548 " pdb=" CA PRO B 548 " pdb=" C PRO B 548 " ideal model delta sigma weight residual 112.47 119.88 -7.41 2.06e+00 2.36e-01 1.29e+01 angle pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.22e+00 angle pdb=" N GLU A 700 " pdb=" CA GLU A 700 " pdb=" CB GLU A 700 " ideal model delta sigma weight residual 110.28 114.72 -4.44 1.55e+00 4.16e-01 8.20e+00 angle pdb=" C LEU D 71 " pdb=" N GLU D 72 " pdb=" CA GLU D 72 " ideal model delta sigma weight residual 121.18 115.78 5.40 1.98e+00 2.55e-01 7.44e+00 ... (remaining 19839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 8057 17.49 - 34.99: 658 34.99 - 52.48: 106 52.48 - 69.98: 27 69.98 - 87.47: 17 Dihedral angle restraints: 8865 sinusoidal: 3692 harmonic: 5173 Sorted by residual: dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 862 " pdb=" CB CYS B 862 " ideal model delta sinusoidal sigma weight residual -86.00 -173.47 87.47 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual -86.00 -161.70 75.70 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 159.21 -66.21 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 8862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1704 0.049 - 0.099: 341 0.099 - 0.148: 102 0.148 - 0.198: 5 0.198 - 0.247: 1 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" C PRO B 548 " pdb=" CB PRO B 548 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 566 " pdb=" N ILE A 566 " pdb=" C ILE A 566 " pdb=" CB ILE A 566 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CB ILE A 370 " pdb=" CA ILE A 370 " pdb=" CG1 ILE A 370 " pdb=" CG2 ILE A 370 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 2150 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 547 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO B 548 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 550 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 551 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 551 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 551 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C THR B 580 " -0.033 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.011 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 687 2.71 - 3.26: 15466 3.26 - 3.81: 25556 3.81 - 4.35: 32486 4.35 - 4.90: 50400 Nonbonded interactions: 124595 Sorted by model distance: nonbonded pdb=" OE1 GLU B 836 " pdb=" OH TYR B 847 " model vdw 2.165 2.440 nonbonded pdb=" NH1 ARG B 853 " pdb=" O PRO B 881 " model vdw 2.177 2.520 nonbonded pdb=" OG SER E 67 " pdb=" OE1 GLN E 70 " model vdw 2.184 2.440 nonbonded pdb=" O THR B 547 " pdb=" N SER B 549 " model vdw 2.193 2.520 nonbonded pdb=" O LEU B 87 " pdb=" OG1 THR B 325 " model vdw 2.194 2.440 ... (remaining 124590 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 'A' and (resid 5 through 518 or resid 527 through 542 or resid 547 throug \ h 658 or resid 705 through 908)) selection = (chain 'B' and (resid 5 through 151 or resid 198 through 201 or resid 208 throug \ h 518 or resid 527 through 908)) } ncs_group { reference = (chain 'C' and (resid 4 through 28 or resid 56 through 76)) selection = chain 'D' selection = (chain 'E' and resid 4 through 76) selection = (chain 'F' and (resid 4 through 28 or resid 56 through 76)) } 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.720 Check model and map are aligned: 0.230 Set scattering table: 0.110 Process input model: 36.900 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.089 14645 Z= 0.164 Angle : 0.582 8.559 19844 Z= 0.309 Chirality : 0.044 0.247 2153 Planarity : 0.004 0.128 2565 Dihedral : 12.979 82.750 5410 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.16 (0.21), residues: 1731 helix: -0.31 (0.34), residues: 239 sheet: -0.85 (0.27), residues: 362 loop : -0.82 (0.20), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2204 time to fit residues: 25.5084 Evaluate side-chains 47 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4434 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 14645 Z= 0.248 Angle : 0.593 10.121 19844 Z= 0.306 Chirality : 0.042 0.253 2153 Planarity : 0.004 0.124 2565 Dihedral : 5.091 28.525 1933 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.03 % Favored : 91.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.08 (0.21), residues: 1731 helix: 0.05 (0.35), residues: 230 sheet: -0.83 (0.26), residues: 368 loop : -0.83 (0.20), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2128 time to fit residues: 19.9732 Evaluate side-chains 41 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 14645 Z= 0.306 Angle : 0.640 9.306 19844 Z= 0.332 Chirality : 0.043 0.259 2153 Planarity : 0.005 0.119 2565 Dihedral : 5.335 28.154 1933 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.30 % Favored : 90.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.23 (0.21), residues: 1731 helix: -0.15 (0.34), residues: 230 sheet: -0.93 (0.26), residues: 358 loop : -0.92 (0.20), residues: 1143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2678 time to fit residues: 23.0813 Evaluate side-chains 41 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 0.0870 chunk 150 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN C 60 GLN D 4 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 14645 Z= 0.275 Angle : 0.614 8.008 19844 Z= 0.319 Chirality : 0.043 0.261 2153 Planarity : 0.005 0.115 2565 Dihedral : 5.309 29.100 1933 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 30.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.32 % Favored : 91.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.30 (0.21), residues: 1731 helix: -0.27 (0.33), residues: 236 sheet: -1.02 (0.26), residues: 369 loop : -0.93 (0.20), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2386 time to fit residues: 20.9425 Evaluate side-chains 40 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 0.0050 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 14645 Z= 0.236 Angle : 0.585 8.116 19844 Z= 0.304 Chirality : 0.043 0.265 2153 Planarity : 0.004 0.112 2565 Dihedral : 5.223 27.624 1933 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 29.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.49 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1731 helix: -0.21 (0.34), residues: 236 sheet: -1.04 (0.26), residues: 369 loop : -0.91 (0.20), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2388 time to fit residues: 20.7985 Evaluate side-chains 39 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 168 optimal weight: 0.0670 chunk 139 optimal weight: 0.0980 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN D 4 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 14645 Z= 0.177 Angle : 0.556 8.485 19844 Z= 0.289 Chirality : 0.043 0.267 2153 Planarity : 0.004 0.108 2565 Dihedral : 5.045 27.280 1933 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.68 % Favored : 92.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.24 (0.21), residues: 1731 helix: -0.27 (0.34), residues: 242 sheet: -0.91 (0.26), residues: 372 loop : -0.90 (0.20), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2285 time to fit residues: 22.5275 Evaluate side-chains 42 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 14645 Z= 0.256 Angle : 0.599 8.376 19844 Z= 0.310 Chirality : 0.043 0.269 2153 Planarity : 0.004 0.105 2565 Dihedral : 5.181 29.426 1933 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.67 % Favored : 91.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.26 (0.21), residues: 1731 helix: -0.23 (0.34), residues: 236 sheet: -0.87 (0.26), residues: 365 loop : -0.95 (0.20), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2642 time to fit residues: 23.4680 Evaluate side-chains 38 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 0.0470 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 14645 Z= 0.203 Angle : 0.563 8.309 19844 Z= 0.292 Chirality : 0.043 0.266 2153 Planarity : 0.004 0.101 2565 Dihedral : 5.076 27.557 1933 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.09 % Favored : 91.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1731 helix: -0.13 (0.34), residues: 236 sheet: -0.80 (0.26), residues: 382 loop : -0.91 (0.20), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2573 time to fit residues: 22.9864 Evaluate side-chains 39 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.0570 chunk 141 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 165 optimal weight: 30.0000 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 14645 Z= 0.157 Angle : 0.540 7.591 19844 Z= 0.281 Chirality : 0.043 0.176 2153 Planarity : 0.003 0.061 2565 Dihedral : 4.877 27.388 1933 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.63 % Favored : 92.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.06 (0.21), residues: 1731 helix: -0.10 (0.34), residues: 236 sheet: -0.59 (0.26), residues: 373 loop : -0.87 (0.20), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2584 time to fit residues: 25.9755 Evaluate side-chains 41 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 173 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 14645 Z= 0.212 Angle : 0.565 8.113 19844 Z= 0.291 Chirality : 0.043 0.182 2153 Planarity : 0.004 0.065 2565 Dihedral : 4.945 27.647 1933 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.32 % Favored : 91.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.09 (0.21), residues: 1731 helix: -0.14 (0.35), residues: 237 sheet: -0.65 (0.26), residues: 378 loop : -0.87 (0.20), residues: 1116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2610 time to fit residues: 23.6002 Evaluate side-chains 37 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 141 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 chunk 121 optimal weight: 0.0040 chunk 7 optimal weight: 0.6980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.019294 restraints weight = 227532.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.020073 restraints weight = 138499.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.020602 restraints weight = 98301.506| |-----------------------------------------------------------------------------| r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 14645 Z= 0.142 Angle : 0.533 8.295 19844 Z= 0.274 Chirality : 0.043 0.172 2153 Planarity : 0.003 0.065 2565 Dihedral : 4.702 26.167 1933 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.01 (0.21), residues: 1731 helix: -0.14 (0.34), residues: 237 sheet: -0.49 (0.26), residues: 378 loop : -0.84 (0.20), residues: 1116 =============================================================================== Job complete usr+sys time: 2159.13 seconds wall clock time: 41 minutes 9.25 seconds (2469.25 seconds total)