Starting phenix.real_space_refine on Sat Jan 20 03:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbe_23252/01_2024/7lbe_23252.pdb" } resolution = 2.9 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= -0.033 sd= 0.634 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8597 2.51 5 N 2258 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13511 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5234 Classifications: {'peptide': 652} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 618} Chain breaks: 3 Chain: "B" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1845 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2484 Classifications: {'peptide': 299} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 280} Chain breaks: 3 Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1001 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 151 Unusual residues: {'MAN': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.31, per 1000 atoms: 0.54 Number of scatterers: 13511 At special positions: 0 Unit cell: (98.6522, 177.033, 166.222, 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 63 16.00 O 2593 8.00 N 2258 7.00 C 8597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " 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 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 55 " " NAG A 803 " - " ASN A 700 " " NAG A 804 " - " ASN A 62 " " NAG A 805 " - " ASN A 67 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 155 " " NAG C 602 " - " ASN C 217 " " NAG C 603 " - " ASN C 240 " " NAG C 604 " - " ASN C 365 " " NAG C 605 " - " ASN C 452 " " NAG C 606 " - " ASN C 128 " " NAG C 607 " - " ASN C 85 " " NAG C 608 " - " ASN C 101 " " NAG C 610 " - " ASN C 383 " " NAG C 611 " - " ASN C 169 " " NAG D 1 " - " ASN C 160 " " NAG I 1 " - " ASN C 348 " " NAG J 1 " - " ASN C 431 " Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 2.2 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 24 sheets defined 31.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.639A pdb=" N GLU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.772A pdb=" N SER A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR A 291 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.716A pdb=" N TYR A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.975A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.669A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 6.000A pdb=" N HIS A 433 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 435 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.644A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.676A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.729A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 644 through 648 removed outlier: 4.333A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.775A pdb=" N LEU B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.834A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 removed outlier: 4.080A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.689A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 215 Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.703A pdb=" N ARG C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.553A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 413 through 436 Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.624A pdb=" N LEU C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.750A pdb=" N VAL E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.906A pdb=" N TYR F 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.959A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 88 Processing helix chain 'H' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.006A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA A 75 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE B 181 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.674A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.460A pdb=" N LEU A 613 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 638 removed outlier: 7.158A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.760A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.980A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 removed outlier: 3.529A pdb=" N ILE C 319 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB6, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 36 removed outlier: 6.489A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.834A pdb=" N ILE F 57 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE F 73 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP F 59 " --> pdb=" O MET F 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 33 through 34 removed outlier: 4.061A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 29 through 30 removed outlier: 3.670A pdb=" N ASP G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.924A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.870A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.932A pdb=" N VAL H 142 " --> pdb=" O ARG H 121 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1413 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: 4.76 Time building geometry restraints manager: 5.74 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: 4275 1.34 - 1.46: 3433 1.46 - 1.58: 6022 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 13825 Sorted by residual: bond pdb=" N ASP A 241 " pdb=" CA ASP A 241 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.51e-02 4.39e+03 4.21e+00 bond pdb=" C1 MAN D 6 " pdb=" C2 MAN D 6 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ASN C 81 " pdb=" CA ASN C 81 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP G 24 " pdb=" CA ASP G 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 13820 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.88: 315 105.88 - 112.92: 7628 112.92 - 119.96: 4579 119.96 - 127.00: 6126 127.00 - 134.04: 161 Bond angle restraints: 18809 Sorted by residual: angle pdb=" N ASP A 241 " pdb=" CA ASP A 241 " pdb=" C ASP A 241 " ideal model delta sigma weight residual 111.39 106.93 4.46 1.38e+00 5.25e-01 1.05e+01 angle pdb=" CA ASP A 241 " pdb=" C ASP A 241 " pdb=" O ASP A 241 " ideal model delta sigma weight residual 121.84 118.67 3.17 1.16e+00 7.43e-01 7.45e+00 angle pdb=" C ASN E 53 " pdb=" N ASN E 54 " pdb=" CA ASN E 54 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.50 6.45 3.00e+00 1.11e-01 4.62e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.38 6.39 3.00e+00 1.11e-01 4.54e+00 ... (remaining 18804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 8089 22.40 - 44.80: 386 44.80 - 67.20: 58 67.20 - 89.60: 27 89.60 - 112.00: 4 Dihedral angle restraints: 8564 sinusoidal: 3700 harmonic: 4864 Sorted by residual: dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -154.60 68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -147.75 61.75 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS C 167 " pdb=" SG CYS C 167 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual 93.00 55.98 37.02 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1868 0.052 - 0.104: 259 0.104 - 0.156: 79 0.156 - 0.208: 4 0.208 - 0.260: 1 Chirality restraints: 2211 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG C 610 " pdb=" ND2 ASN C 383 " pdb=" C2 NAG C 610 " pdb=" O5 NAG C 610 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 365 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 2208 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 124 " -0.152 9.50e-02 1.11e+02 6.86e-02 3.34e+00 pdb=" NE ARG F 124 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 124 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 124 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 92 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 93 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 180 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 181 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.018 5.00e-02 4.00e+02 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 13668 3.28 - 3.82: 21854 3.82 - 4.36: 27222 4.36 - 4.90: 46951 Nonbonded interactions: 110773 Sorted by model distance: nonbonded pdb=" NH2 ARG H 90 " pdb=" OD2 ASP H 113 " model vdw 2.200 2.520 nonbonded pdb=" O PHE H 52 " pdb=" NH2 ARG H 95 " model vdw 2.202 2.520 nonbonded pdb=" O VAL A 256 " pdb=" NH2 ARG A 264 " model vdw 2.222 2.520 nonbonded pdb=" OD2 ASP A 445 " pdb=" OH TYR H 125 " model vdw 2.271 2.440 nonbonded pdb=" O TRP A 167 " pdb=" NE2 GLN A 442 " model vdw 2.281 2.520 ... (remaining 110768 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 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.820 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.980 Find NCS groups from input model: 0.400 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 0.037 13825 Z= 0.204 Angle : 0.515 6.446 18809 Z= 0.244 Chirality : 0.042 0.260 2211 Planarity : 0.003 0.069 2358 Dihedral : 13.527 111.996 5384 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.20 (0.22), residues: 1625 helix: 1.96 (0.27), residues: 391 sheet: 0.89 (0.27), residues: 381 loop : 0.30 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.002 0.000 HIS A 289 PHE 0.010 0.001 PHE F 123 TYR 0.015 0.001 TYR B 226 ARG 0.012 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8383 (mmm) cc_final: 0.8170 (mmm) REVERT: A 107 ASN cc_start: 0.8516 (m-40) cc_final: 0.8257 (m-40) REVERT: A 329 ARG cc_start: 0.8151 (mmp-170) cc_final: 0.7832 (mmp-170) REVERT: B 239 ASP cc_start: 0.8062 (t0) cc_final: 0.7783 (t0) REVERT: F 85 GLN cc_start: 0.7996 (tp40) cc_final: 0.7570 (tp40) REVERT: G 53 LEU cc_start: 0.9211 (tp) cc_final: 0.8966 (tp) REVERT: G 100 THR cc_start: 0.8549 (m) cc_final: 0.8289 (t) REVERT: H 96 ASP cc_start: 0.8217 (t70) cc_final: 0.7549 (t70) REVERT: H 100 ASN cc_start: 0.8980 (t0) cc_final: 0.8720 (t0) REVERT: H 128 PHE cc_start: 0.8751 (t80) cc_final: 0.8546 (t80) REVERT: H 141 ASP cc_start: 0.8859 (p0) cc_final: 0.8522 (p0) REVERT: H 145 GLN cc_start: 0.8422 (mm110) cc_final: 0.8208 (mm-40) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.1390 time to fit residues: 389.0117 Evaluate side-chains 232 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 451 HIS C 91 GLN C 358 ASN E 54 ASN F 26 GLN G 81 ASN H 107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13825 Z= 0.291 Angle : 0.583 8.038 18809 Z= 0.298 Chirality : 0.045 0.189 2211 Planarity : 0.004 0.047 2358 Dihedral : 8.246 89.489 2302 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.11 % Allowed : 11.86 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.22), residues: 1625 helix: 1.83 (0.27), residues: 384 sheet: 0.83 (0.27), residues: 383 loop : 0.27 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 330 HIS 0.008 0.001 HIS A 451 PHE 0.017 0.002 PHE C 412 TYR 0.015 0.002 TYR B 226 ARG 0.008 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8445 (mmm) cc_final: 0.8240 (mmm) REVERT: A 329 ARG cc_start: 0.8255 (mmp-170) cc_final: 0.8018 (mmp-170) REVERT: A 598 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7959 (mmmt) REVERT: A 656 GLU cc_start: 0.8310 (tt0) cc_final: 0.8083 (tt0) REVERT: A 669 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8485 (mtp) REVERT: A 680 ASP cc_start: 0.8692 (t0) cc_final: 0.8317 (t0) REVERT: B 225 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8903 (mm) REVERT: E 29 GLN cc_start: 0.8617 (tt0) cc_final: 0.8367 (tt0) REVERT: E 47 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8440 (mtp-110) REVERT: E 61 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8722 (tp40) REVERT: E 65 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7612 (mtmt) REVERT: F 42 LYS cc_start: 0.9325 (tptm) cc_final: 0.9066 (tptp) REVERT: F 85 GLN cc_start: 0.8132 (tp40) cc_final: 0.7787 (tp40) REVERT: F 124 ARG cc_start: 0.8449 (mmt-90) cc_final: 0.7716 (mmt180) REVERT: G 53 LEU cc_start: 0.9199 (tp) cc_final: 0.8952 (tp) REVERT: G 81 ASN cc_start: 0.7928 (m110) cc_final: 0.7541 (m110) REVERT: G 100 THR cc_start: 0.8599 (m) cc_final: 0.8252 (t) REVERT: H 100 ASN cc_start: 0.8737 (t0) cc_final: 0.8482 (t0) REVERT: H 141 ASP cc_start: 0.8799 (p0) cc_final: 0.8585 (p0) outliers start: 31 outliers final: 14 residues processed: 257 average time/residue: 1.1079 time to fit residues: 314.4604 Evaluate side-chains 242 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 358 ASN C 360 HIS E 54 ASN F 54 ASN H 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13825 Z= 0.379 Angle : 0.611 8.804 18809 Z= 0.309 Chirality : 0.046 0.211 2211 Planarity : 0.005 0.037 2358 Dihedral : 7.960 85.439 2302 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.61 % Allowed : 13.63 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.65 (0.21), residues: 1625 helix: 1.50 (0.26), residues: 385 sheet: 0.56 (0.27), residues: 380 loop : -0.04 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 462 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.002 PHE B 105 TYR 0.019 0.002 TYR A 682 ARG 0.009 0.001 ARG H 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 220 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8453 (mmm) cc_final: 0.8211 (mmm) REVERT: A 329 ARG cc_start: 0.8502 (mmp-170) cc_final: 0.8185 (mmp-170) REVERT: A 669 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: A 680 ASP cc_start: 0.8622 (t0) cc_final: 0.8245 (t0) REVERT: B 225 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8908 (mm) REVERT: C 105 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8615 (p) REVERT: E 47 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8301 (mtp-110) REVERT: E 61 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8455 (tp40) REVERT: E 65 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7730 (mtmt) REVERT: E 104 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: F 85 GLN cc_start: 0.8172 (tp40) cc_final: 0.7780 (tp40) REVERT: G 53 LEU cc_start: 0.9227 (tp) cc_final: 0.8983 (tp) REVERT: G 100 THR cc_start: 0.8626 (m) cc_final: 0.8226 (t) REVERT: H 36 LYS cc_start: 0.6578 (tptt) cc_final: 0.6056 (mmmt) REVERT: H 100 ASN cc_start: 0.8696 (t0) cc_final: 0.8427 (t0) REVERT: H 106 MET cc_start: 0.8786 (mtm) cc_final: 0.8556 (mtp) outliers start: 53 outliers final: 27 residues processed: 250 average time/residue: 1.0684 time to fit residues: 296.1533 Evaluate side-chains 250 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS E 54 ASN F 54 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13825 Z= 0.322 Angle : 0.595 12.695 18809 Z= 0.297 Chirality : 0.045 0.216 2211 Planarity : 0.004 0.034 2358 Dihedral : 7.608 77.162 2302 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.68 % Allowed : 16.02 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.56 (0.21), residues: 1625 helix: 1.45 (0.26), residues: 385 sheet: 0.49 (0.27), residues: 382 loop : -0.10 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 330 HIS 0.003 0.001 HIS A 451 PHE 0.019 0.002 PHE B 105 TYR 0.014 0.002 TYR B 226 ARG 0.006 0.001 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8459 (mmm) cc_final: 0.8207 (mmm) REVERT: A 329 ARG cc_start: 0.8420 (mmp-170) cc_final: 0.8194 (mmp-170) REVERT: A 507 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9016 (tt) REVERT: A 669 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8628 (mtp) REVERT: A 680 ASP cc_start: 0.8590 (t0) cc_final: 0.8220 (t0) REVERT: B 117 ASP cc_start: 0.7590 (t70) cc_final: 0.7267 (t70) REVERT: B 225 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8896 (mm) REVERT: C 105 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 197 ASP cc_start: 0.8134 (p0) cc_final: 0.7861 (p0) REVERT: E 45 THR cc_start: 0.9174 (m) cc_final: 0.8916 (m) REVERT: E 47 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8408 (mtp-110) REVERT: E 61 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: E 65 LYS cc_start: 0.8569 (mtpt) cc_final: 0.7901 (mtmt) REVERT: E 77 LEU cc_start: 0.9285 (tp) cc_final: 0.9025 (tm) REVERT: F 42 LYS cc_start: 0.9300 (tptm) cc_final: 0.9082 (tptp) REVERT: F 85 GLN cc_start: 0.8180 (tp40) cc_final: 0.7774 (tp40) REVERT: G 28 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (p) REVERT: G 53 LEU cc_start: 0.9230 (tp) cc_final: 0.8988 (tp) REVERT: G 100 THR cc_start: 0.8626 (m) cc_final: 0.8221 (t) REVERT: H 36 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6035 (mmmt) REVERT: H 43 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8673 (mp) REVERT: H 100 ASN cc_start: 0.8664 (t0) cc_final: 0.8408 (t0) outliers start: 54 outliers final: 30 residues processed: 255 average time/residue: 1.0406 time to fit residues: 295.0833 Evaluate side-chains 257 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN E 54 ASN E 102 GLN F 54 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13825 Z= 0.297 Angle : 0.579 11.616 18809 Z= 0.291 Chirality : 0.044 0.216 2211 Planarity : 0.004 0.033 2358 Dihedral : 7.348 70.712 2302 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.70 % Allowed : 15.95 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.55 (0.21), residues: 1625 helix: 1.51 (0.27), residues: 379 sheet: 0.42 (0.27), residues: 380 loop : -0.10 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 330 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.002 PHE B 105 TYR 0.019 0.001 TYR A 682 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 220 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8459 (mmm) cc_final: 0.8220 (mmm) REVERT: A 329 ARG cc_start: 0.8428 (mmp-170) cc_final: 0.8173 (mmp-170) REVERT: A 507 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (tt) REVERT: B 117 ASP cc_start: 0.7594 (t70) cc_final: 0.7327 (t70) REVERT: B 225 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8885 (mm) REVERT: C 105 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8763 (p) REVERT: E 45 THR cc_start: 0.9173 (m) cc_final: 0.8913 (m) REVERT: E 47 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8386 (mtp-110) REVERT: E 61 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8763 (tp40) REVERT: E 65 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7865 (mtmt) REVERT: E 77 LEU cc_start: 0.9378 (tp) cc_final: 0.9145 (tm) REVERT: E 104 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: F 85 GLN cc_start: 0.8133 (tp40) cc_final: 0.7785 (tp40) REVERT: G 53 LEU cc_start: 0.9229 (tp) cc_final: 0.8986 (tp) REVERT: H 36 LYS cc_start: 0.6538 (tptt) cc_final: 0.6008 (mmmt) REVERT: H 100 ASN cc_start: 0.8650 (t0) cc_final: 0.8390 (t0) outliers start: 69 outliers final: 32 residues processed: 262 average time/residue: 1.0463 time to fit residues: 304.4259 Evaluate side-chains 255 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 431 GLN E 54 ASN F 54 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13825 Z= 0.189 Angle : 0.548 11.914 18809 Z= 0.276 Chirality : 0.043 0.203 2211 Planarity : 0.004 0.033 2358 Dihedral : 6.695 52.869 2302 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 17.72 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.64 (0.22), residues: 1625 helix: 1.59 (0.27), residues: 384 sheet: 0.42 (0.27), residues: 382 loop : -0.03 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.001 PHE B 105 TYR 0.013 0.001 TYR B 226 ARG 0.005 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8425 (mmm) cc_final: 0.8188 (mmm) REVERT: A 241 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: A 329 ARG cc_start: 0.8409 (mmp-170) cc_final: 0.8164 (mmp-170) REVERT: A 337 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 598 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7849 (mmmt) REVERT: B 117 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7327 (t70) REVERT: C 84 MET cc_start: 0.6965 (ptm) cc_final: 0.6716 (ptt) REVERT: C 332 TYR cc_start: 0.9030 (m-80) cc_final: 0.8819 (m-10) REVERT: E 28 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8677 (p) REVERT: E 45 THR cc_start: 0.9158 (m) cc_final: 0.8917 (m) REVERT: E 47 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8302 (mtp-110) REVERT: E 65 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8275 (mtmt) REVERT: E 102 GLN cc_start: 0.8332 (mm110) cc_final: 0.7975 (mm-40) REVERT: E 104 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: F 42 LYS cc_start: 0.9165 (tptm) cc_final: 0.8913 (tptp) REVERT: F 85 GLN cc_start: 0.8153 (tp40) cc_final: 0.7790 (tp40) REVERT: F 138 GLN cc_start: 0.8883 (pm20) cc_final: 0.8647 (pm20) REVERT: G 53 LEU cc_start: 0.9229 (tp) cc_final: 0.8983 (tp) REVERT: G 100 THR cc_start: 0.8614 (m) cc_final: 0.8216 (t) REVERT: H 100 ASN cc_start: 0.8613 (t0) cc_final: 0.8401 (t0) outliers start: 46 outliers final: 22 residues processed: 258 average time/residue: 1.0285 time to fit residues: 295.6469 Evaluate side-chains 250 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 87 optimal weight: 0.0470 chunk 156 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN E 54 ASN E 102 GLN H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13825 Z= 0.166 Angle : 0.542 11.851 18809 Z= 0.270 Chirality : 0.042 0.202 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.178 53.015 2302 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.86 % Allowed : 18.81 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.71 (0.22), residues: 1625 helix: 1.63 (0.27), residues: 384 sheet: 0.46 (0.27), residues: 382 loop : 0.03 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE B 105 TYR 0.021 0.001 TYR A 682 ARG 0.005 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8409 (mmm) cc_final: 0.8171 (mmm) REVERT: A 241 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: A 329 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.8136 (mmp-170) REVERT: A 337 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7960 (p) REVERT: A 598 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7836 (mmmt) REVERT: A 680 ASP cc_start: 0.8473 (t0) cc_final: 0.8081 (t0) REVERT: B 117 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7317 (t70) REVERT: C 84 MET cc_start: 0.6920 (ptm) cc_final: 0.6685 (ptt) REVERT: C 146 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8569 (m) REVERT: E 28 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8668 (p) REVERT: E 45 THR cc_start: 0.9142 (m) cc_final: 0.8903 (m) REVERT: E 47 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8285 (mtp-110) REVERT: E 50 GLN cc_start: 0.8510 (mt0) cc_final: 0.8143 (mm-40) REVERT: E 65 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8139 (mtmt) REVERT: F 42 LYS cc_start: 0.9231 (tptm) cc_final: 0.9025 (tptp) REVERT: F 85 GLN cc_start: 0.8122 (tp40) cc_final: 0.7783 (tp40) REVERT: F 138 GLN cc_start: 0.8848 (pm20) cc_final: 0.8619 (pm20) REVERT: G 53 LEU cc_start: 0.9223 (tp) cc_final: 0.8958 (tp) REVERT: G 100 THR cc_start: 0.8603 (m) cc_final: 0.8210 (t) REVERT: H 100 ASN cc_start: 0.8581 (t0) cc_final: 0.8377 (t0) outliers start: 42 outliers final: 21 residues processed: 253 average time/residue: 1.0233 time to fit residues: 287.6901 Evaluate side-chains 246 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 77 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 122 optimal weight: 0.0270 chunk 142 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 102 GLN H 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13825 Z= 0.191 Angle : 0.545 11.613 18809 Z= 0.272 Chirality : 0.043 0.199 2211 Planarity : 0.004 0.040 2358 Dihedral : 6.055 53.489 2302 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.00 % Allowed : 18.20 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.70 (0.22), residues: 1625 helix: 1.59 (0.27), residues: 384 sheet: 0.48 (0.27), residues: 382 loop : 0.03 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 330 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.001 PHE B 105 TYR 0.012 0.001 TYR B 226 ARG 0.004 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8428 (mmm) cc_final: 0.8199 (mmm) REVERT: A 241 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: A 329 ARG cc_start: 0.8364 (mmp-170) cc_final: 0.8104 (mmp-170) REVERT: A 337 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7969 (p) REVERT: A 598 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7838 (mmmt) REVERT: A 680 ASP cc_start: 0.8469 (t0) cc_final: 0.8072 (t0) REVERT: B 117 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7332 (t70) REVERT: C 84 MET cc_start: 0.6888 (ptm) cc_final: 0.6638 (ptt) REVERT: E 28 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (p) REVERT: E 45 THR cc_start: 0.9143 (m) cc_final: 0.8910 (m) REVERT: E 47 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8223 (mtp-110) REVERT: E 50 GLN cc_start: 0.8455 (mt0) cc_final: 0.8094 (mm-40) REVERT: E 65 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8135 (mtmt) REVERT: F 42 LYS cc_start: 0.9223 (tptm) cc_final: 0.8981 (tptp) REVERT: F 85 GLN cc_start: 0.8099 (tp40) cc_final: 0.7778 (tp40) REVERT: F 138 GLN cc_start: 0.8832 (pm20) cc_final: 0.8614 (pm20) REVERT: G 53 LEU cc_start: 0.9222 (tp) cc_final: 0.8964 (tp) REVERT: G 100 THR cc_start: 0.8594 (m) cc_final: 0.8203 (t) outliers start: 44 outliers final: 28 residues processed: 257 average time/residue: 1.0500 time to fit residues: 301.2880 Evaluate side-chains 251 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 77 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN E 54 ASN H 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13825 Z= 0.194 Angle : 0.552 11.669 18809 Z= 0.276 Chirality : 0.043 0.202 2211 Planarity : 0.004 0.037 2358 Dihedral : 6.000 53.453 2302 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.73 % Allowed : 18.81 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.22), residues: 1625 helix: 1.57 (0.27), residues: 384 sheet: 0.49 (0.27), residues: 380 loop : 0.01 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 462 HIS 0.002 0.001 HIS A 213 PHE 0.015 0.001 PHE B 105 TYR 0.021 0.001 TYR A 682 ARG 0.004 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8430 (mmm) cc_final: 0.8195 (mmm) REVERT: A 111 LEU cc_start: 0.8613 (mp) cc_final: 0.8386 (mt) REVERT: A 241 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: A 329 ARG cc_start: 0.8365 (mmp-170) cc_final: 0.8101 (mmp-170) REVERT: A 337 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7959 (p) REVERT: A 598 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7832 (mmmt) REVERT: A 680 ASP cc_start: 0.8482 (t0) cc_final: 0.8085 (t0) REVERT: B 117 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7342 (t70) REVERT: C 84 MET cc_start: 0.6890 (ptm) cc_final: 0.6642 (ptt) REVERT: C 146 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8770 (m) REVERT: E 28 THR cc_start: 0.8898 (m) cc_final: 0.8602 (p) REVERT: E 45 THR cc_start: 0.9126 (m) cc_final: 0.8898 (m) REVERT: E 47 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.7995 (mtp-110) REVERT: E 50 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8088 (mm-40) REVERT: E 65 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8131 (mtmt) REVERT: F 42 LYS cc_start: 0.9251 (tptm) cc_final: 0.8976 (tptp) REVERT: F 85 GLN cc_start: 0.8096 (tp40) cc_final: 0.7773 (tp40) REVERT: G 32 LEU cc_start: 0.8983 (mt) cc_final: 0.8753 (mm) REVERT: G 53 LEU cc_start: 0.9190 (tp) cc_final: 0.8947 (tp) REVERT: G 100 THR cc_start: 0.8595 (m) cc_final: 0.8208 (t) REVERT: H 101 SER cc_start: 0.9333 (p) cc_final: 0.9069 (m) outliers start: 40 outliers final: 27 residues processed: 252 average time/residue: 1.0897 time to fit residues: 305.7336 Evaluate side-chains 255 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN H 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13825 Z= 0.186 Angle : 0.557 12.195 18809 Z= 0.279 Chirality : 0.043 0.201 2211 Planarity : 0.004 0.036 2358 Dihedral : 5.950 53.725 2302 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.32 % Allowed : 19.56 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.69 (0.22), residues: 1625 helix: 1.55 (0.27), residues: 384 sheet: 0.46 (0.27), residues: 382 loop : 0.05 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE B 105 TYR 0.013 0.001 TYR B 169 ARG 0.007 0.000 ARG H 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8404 (mmm) cc_final: 0.8171 (mmm) REVERT: A 111 LEU cc_start: 0.8596 (mp) cc_final: 0.8367 (mt) REVERT: A 241 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: A 329 ARG cc_start: 0.8364 (mmp-170) cc_final: 0.8099 (mmp-170) REVERT: A 337 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 598 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7828 (mmmt) REVERT: B 117 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7352 (t70) REVERT: C 84 MET cc_start: 0.6907 (ptm) cc_final: 0.6655 (ptt) REVERT: E 28 THR cc_start: 0.8966 (m) cc_final: 0.8581 (p) REVERT: E 45 THR cc_start: 0.9135 (m) cc_final: 0.8907 (m) REVERT: E 47 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.7980 (mtp-110) REVERT: E 50 GLN cc_start: 0.8400 (mt0) cc_final: 0.8028 (mm-40) REVERT: E 65 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8125 (mtmt) REVERT: F 42 LYS cc_start: 0.9250 (tptm) cc_final: 0.8978 (tptp) REVERT: F 85 GLN cc_start: 0.8089 (tp40) cc_final: 0.7783 (tp40) REVERT: G 32 LEU cc_start: 0.8974 (mt) cc_final: 0.8755 (mm) REVERT: G 53 LEU cc_start: 0.9182 (tp) cc_final: 0.8933 (tp) REVERT: G 100 THR cc_start: 0.8591 (m) cc_final: 0.8206 (t) REVERT: H 141 ASP cc_start: 0.8846 (p0) cc_final: 0.8568 (p0) outliers start: 34 outliers final: 27 residues processed: 248 average time/residue: 1.0364 time to fit residues: 285.7994 Evaluate side-chains 247 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN E 54 ASN F 138 GLN H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089069 restraints weight = 24806.773| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.58 r_work: 0.3061 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13825 Z= 0.357 Angle : 0.624 10.680 18809 Z= 0.313 Chirality : 0.046 0.234 2211 Planarity : 0.004 0.037 2358 Dihedral : 6.207 55.378 2302 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.25 % Allowed : 19.84 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.46 (0.21), residues: 1625 helix: 1.45 (0.27), residues: 379 sheet: 0.24 (0.27), residues: 381 loop : -0.10 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 462 HIS 0.005 0.001 HIS A 451 PHE 0.016 0.002 PHE B 105 TYR 0.022 0.002 TYR A 682 ARG 0.007 0.001 ARG H 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.61 seconds wall clock time: 93 minutes 27.02 seconds (5607.02 seconds total)