Starting phenix.real_space_refine on Mon Mar 18 10:33:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/03_2024/8eyy_28724_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/03_2024/8eyy_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_28724/03_2024/8eyy_28724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/03_2024/8eyy_28724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/03_2024/8eyy_28724_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyy_28724/03_2024/8eyy_28724_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-dev-5265/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: 7.08, 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: 5.20 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: 1.51 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: 6.29 Time building geometry restraints manager: 5.65 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.110 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- 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 % Allowed : 0.37 % Favored : 99.57 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.005 0.001 HIS B 386 PHE 0.015 0.001 PHE A 703 TYR 0.012 0.001 TYR E 16 ARG 0.013 0.000 ARG B 479 *********************** 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 : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 LEU cc_start: 0.8598 (mt) cc_final: 0.8392 (mt) REVERT: A 504 MET cc_start: 0.7752 (tpt) cc_final: 0.7438 (tpt) REVERT: A 555 MET cc_start: 0.9449 (mmp) cc_final: 0.9105 (mmp) REVERT: B 11 MET cc_start: 0.8731 (ppp) cc_final: 0.8237 (ppp) REVERT: B 38 MET cc_start: 0.9406 (mmp) cc_final: 0.9198 (mmm) REVERT: B 62 LEU cc_start: 0.9678 (tp) cc_final: 0.9442 (tp) REVERT: B 98 MET cc_start: 0.8915 (mmp) cc_final: 0.8497 (mmm) REVERT: B 110 MET cc_start: 0.9241 (mmp) cc_final: 0.8880 (mmm) REVERT: F 6 LEU cc_start: 0.9412 (mm) cc_final: 0.9156 (pt) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2060 time to fit residues: 24.1256 Evaluate side-chains 49 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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: 0.9990 chunk 88 optimal weight: 7.9990 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: 2.7588 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14645 Z= 0.208 Angle : 0.564 8.960 19844 Z= 0.293 Chirality : 0.042 0.253 2153 Planarity : 0.004 0.124 2565 Dihedral : 4.986 28.417 1933 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.86 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -0.02 (0.35), residues: 236 sheet: -0.76 (0.26), residues: 373 loop : -0.82 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.004 0.001 HIS A 386 PHE 0.013 0.001 PHE A 703 TYR 0.016 0.001 TYR B 144 ARG 0.010 0.000 ARG B 479 *********************** 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 56 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8925 (mmp) cc_final: 0.8599 (mmm) REVERT: A 504 MET cc_start: 0.7659 (tpt) cc_final: 0.7332 (tpt) REVERT: A 555 MET cc_start: 0.9494 (mmp) cc_final: 0.9116 (mmp) REVERT: B 98 MET cc_start: 0.9148 (mmp) cc_final: 0.8822 (mmm) REVERT: F 6 LEU cc_start: 0.9400 (mm) cc_final: 0.9137 (pt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2200 time to fit residues: 21.3123 Evaluate side-chains 41 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 406 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 14645 Z= 0.357 Angle : 0.691 10.987 19844 Z= 0.355 Chirality : 0.044 0.260 2153 Planarity : 0.005 0.119 2565 Dihedral : 5.445 28.586 1933 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 35.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.42 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % 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: -0.26 (0.33), residues: 230 sheet: -0.96 (0.26), residues: 358 loop : -0.93 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 414 HIS 0.012 0.002 HIS B 199 PHE 0.020 0.002 PHE A 400 TYR 0.017 0.002 TYR B 245 ARG 0.009 0.001 ARG B 345 *********************** 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 49 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8996 (mmp) cc_final: 0.8677 (mmm) REVERT: A 504 MET cc_start: 0.7593 (tpt) cc_final: 0.7294 (tpt) REVERT: A 555 MET cc_start: 0.9529 (mmp) cc_final: 0.9168 (mmp) REVERT: B 62 LEU cc_start: 0.9541 (tp) cc_final: 0.9328 (tp) REVERT: B 98 MET cc_start: 0.9259 (mmp) cc_final: 0.8912 (mmm) REVERT: F 6 LEU cc_start: 0.9431 (mm) cc_final: 0.9154 (pt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2300 time to fit residues: 19.6831 Evaluate side-chains 39 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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: 7.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 0.0370 chunk 150 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 140 optimal weight: 0.0370 overall best weight: 3.2142 ------------------------------------------------------------------------------- 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** 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: 0.8299 moved from start: 0.1372 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= 0.227 Angle : 0.581 7.962 19844 Z= 0.304 Chirality : 0.043 0.260 2153 Planarity : 0.004 0.115 2565 Dihedral : 5.251 28.602 1933 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.80 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -1.25 (0.21), residues: 1731 helix: -0.20 (0.34), residues: 236 sheet: -0.94 (0.26), residues: 369 loop : -0.93 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 414 HIS 0.006 0.001 HIS A 758 PHE 0.016 0.002 PHE A 703 TYR 0.016 0.001 TYR E 16 ARG 0.012 0.001 ARG B 479 *********************** 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 52 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.9611 (mpp) cc_final: 0.9397 (mpp) REVERT: A 38 MET cc_start: 0.9012 (mmp) cc_final: 0.8637 (mmm) REVERT: A 504 MET cc_start: 0.7694 (tpt) cc_final: 0.7330 (tpt) REVERT: A 555 MET cc_start: 0.9419 (mmp) cc_final: 0.9188 (mmp) REVERT: B 11 MET cc_start: 0.9122 (ppp) cc_final: 0.8920 (ppp) REVERT: B 38 MET cc_start: 0.9454 (mmp) cc_final: 0.9228 (mmm) REVERT: B 98 MET cc_start: 0.9212 (mmp) cc_final: 0.8858 (mmm) REVERT: B 300 MET cc_start: 0.9305 (mmp) cc_final: 0.9099 (mmm) REVERT: F 6 LEU cc_start: 0.9455 (mm) cc_final: 0.9155 (pt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2206 time to fit residues: 20.1141 Evaluate side-chains 40 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 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** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1638 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= 0.275 Angle : 0.614 8.247 19844 Z= 0.318 Chirality : 0.043 0.265 2153 Planarity : 0.005 0.112 2565 Dihedral : 5.313 27.185 1933 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.13 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -1.31 (0.21), residues: 1731 helix: -0.25 (0.34), residues: 236 sheet: -1.06 (0.26), residues: 369 loop : -0.93 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 414 HIS 0.005 0.001 HIS B 777 PHE 0.015 0.002 PHE A 400 TYR 0.029 0.002 TYR B 847 ARG 0.009 0.001 ARG B 479 *********************** 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 48 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9033 (mmp) cc_final: 0.8657 (mmm) REVERT: A 504 MET cc_start: 0.7656 (tpt) cc_final: 0.7275 (tpt) REVERT: A 555 MET cc_start: 0.9440 (mmp) cc_final: 0.9222 (mmp) REVERT: B 38 MET cc_start: 0.9453 (mmp) cc_final: 0.9188 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2084 time to fit residues: 17.4650 Evaluate side-chains 36 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** 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: 0.8273 moved from start: 0.1543 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= 0.164 Angle : 0.552 8.542 19844 Z= 0.287 Chirality : 0.043 0.267 2153 Planarity : 0.004 0.109 2565 Dihedral : 5.027 27.702 1933 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -1.17 (0.21), residues: 1731 helix: -0.16 (0.34), residues: 236 sheet: -0.87 (0.26), residues: 370 loop : -0.86 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS B 777 PHE 0.021 0.001 PHE B 868 TYR 0.023 0.001 TYR B 847 ARG 0.008 0.000 ARG A 498 *********************** 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 60 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.9578 (mpp) cc_final: 0.9374 (mpp) REVERT: A 38 MET cc_start: 0.9097 (mmp) cc_final: 0.8686 (mmm) REVERT: B 11 MET cc_start: 0.9117 (ppp) cc_final: 0.8807 (ppp) REVERT: B 38 MET cc_start: 0.9459 (mmp) cc_final: 0.9201 (mmm) REVERT: B 300 MET cc_start: 0.9228 (mmp) cc_final: 0.9015 (mmm) REVERT: F 6 LEU cc_start: 0.9473 (mm) cc_final: 0.9163 (pt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2171 time to fit residues: 22.3563 Evaluate side-chains 43 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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: 20.0000 chunk 95 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 141 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 431 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 337 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: 0.8262 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 14645 Z= 0.144 Angle : 0.535 8.810 19844 Z= 0.277 Chirality : 0.043 0.271 2153 Planarity : 0.004 0.105 2565 Dihedral : 4.769 26.396 1933 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.39 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -1.10 (0.21), residues: 1731 helix: -0.25 (0.34), residues: 242 sheet: -0.66 (0.26), residues: 372 loop : -0.85 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.003 0.001 HIS A 263 PHE 0.015 0.001 PHE A 703 TYR 0.018 0.001 TYR B 847 ARG 0.006 0.000 ARG A 498 *********************** 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 63 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9086 (mmp) cc_final: 0.8642 (mmm) REVERT: B 11 MET cc_start: 0.9022 (ppp) cc_final: 0.8722 (ppp) REVERT: B 38 MET cc_start: 0.9465 (mmp) cc_final: 0.9200 (mmm) REVERT: E 15 LEU cc_start: 0.9732 (tp) cc_final: 0.9531 (tp) REVERT: F 6 LEU cc_start: 0.9446 (mm) cc_final: 0.9146 (pt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2230 time to fit residues: 23.8727 Evaluate side-chains 47 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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: 0.0060 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 40.0000 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 337 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: 0.8277 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14645 Z= 0.162 Angle : 0.528 8.474 19844 Z= 0.273 Chirality : 0.043 0.271 2153 Planarity : 0.004 0.101 2565 Dihedral : 4.723 26.992 1933 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -1.07 (0.21), residues: 1731 helix: -0.21 (0.34), residues: 242 sheet: -0.64 (0.26), residues: 375 loop : -0.83 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS B 777 PHE 0.013 0.001 PHE A 703 TYR 0.018 0.001 TYR B 847 ARG 0.005 0.000 ARG B 479 *********************** 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 59 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9121 (mmp) cc_final: 0.8667 (mmm) REVERT: A 504 MET cc_start: 0.7539 (tpt) cc_final: 0.7304 (tpt) REVERT: A 555 MET cc_start: 0.9399 (mmp) cc_final: 0.9162 (mmp) REVERT: B 11 MET cc_start: 0.8969 (ppp) cc_final: 0.8700 (ppp) REVERT: B 38 MET cc_start: 0.9444 (mmp) cc_final: 0.9183 (mmm) REVERT: B 300 MET cc_start: 0.9231 (mmp) cc_final: 0.8960 (mmm) REVERT: F 6 LEU cc_start: 0.9426 (mm) cc_final: 0.9122 (pt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2300 time to fit residues: 22.4803 Evaluate side-chains 44 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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: 6.9990 chunk 160 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 165 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** ** B 34 GLN ** 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** 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: 0.8316 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14645 Z= 0.257 Angle : 0.602 8.373 19844 Z= 0.309 Chirality : 0.043 0.188 2153 Planarity : 0.004 0.083 2565 Dihedral : 5.015 26.943 1933 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.84 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.13 (0.21), residues: 1731 helix: -0.32 (0.34), residues: 243 sheet: -0.64 (0.26), residues: 366 loop : -0.87 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 414 HIS 0.005 0.001 HIS B 777 PHE 0.016 0.002 PHE A 400 TYR 0.018 0.002 TYR B 847 ARG 0.006 0.001 ARG B 479 *********************** 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 54 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9140 (mmp) cc_final: 0.8692 (mmm) REVERT: A 555 MET cc_start: 0.9430 (mmp) cc_final: 0.9176 (mmp) REVERT: B 38 MET cc_start: 0.9423 (mmp) cc_final: 0.9151 (mmm) REVERT: B 300 MET cc_start: 0.9241 (mmp) cc_final: 0.9036 (mmm) REVERT: F 6 LEU cc_start: 0.9452 (mm) cc_final: 0.9133 (pt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2455 time to fit residues: 22.2834 Evaluate side-chains 38 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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: 0.3980 chunk 78 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 431 ASN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14645 Z= 0.144 Angle : 0.539 8.297 19844 Z= 0.278 Chirality : 0.043 0.176 2153 Planarity : 0.003 0.060 2565 Dihedral : 4.734 27.061 1933 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.96 (0.21), residues: 1731 helix: -0.07 (0.34), residues: 236 sheet: -0.44 (0.26), residues: 373 loop : -0.82 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.003 0.001 HIS A 440 PHE 0.017 0.001 PHE B 382 TYR 0.016 0.001 TYR B 847 ARG 0.005 0.000 ARG B 479 ********************** 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 62 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9153 (mmp) cc_final: 0.8693 (mmm) REVERT: B 11 MET cc_start: 0.8920 (ppp) cc_final: 0.8447 (ppp) REVERT: B 38 MET cc_start: 0.9494 (mmp) cc_final: 0.9224 (mmm) REVERT: B 300 MET cc_start: 0.9191 (mmp) cc_final: 0.8987 (mmm) REVERT: F 6 LEU cc_start: 0.9481 (mm) cc_final: 0.9119 (pt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2186 time to fit residues: 22.8523 Evaluate side-chains 49 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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: 9.9990 chunk 127 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 57 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 7 optimal weight: 0.0070 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 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 = 0.2982 r_free = 0.2982 target = 0.029437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.019181 restraints weight = 217387.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.019979 restraints weight = 133080.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020535 restraints weight = 94539.601| |-----------------------------------------------------------------------------| r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14645 Z= 0.139 Angle : 0.528 10.307 19844 Z= 0.270 Chirality : 0.043 0.165 2153 Planarity : 0.003 0.065 2565 Dihedral : 4.591 30.400 1933 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1731 helix: -0.02 (0.35), residues: 236 sheet: -0.29 (0.27), residues: 363 loop : -0.80 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 100 PHE 0.012 0.001 PHE F 24 TYR 0.014 0.001 TYR B 847 ARG 0.009 0.000 ARG B 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.24 seconds wall clock time: 43 minutes 5.02 seconds (2585.02 seconds total)