Starting phenix.real_space_refine on Sat Feb 17 08:52:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7o_10110/02_2024/6s7o_10110_updated.pdb" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 11889 2.51 5 N 2826 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 263": "NH1" <-> "NH2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 278": "NH1" <-> "NH2" Residue "E ARG 317": "NH1" <-> "NH2" Residue "E ARG 354": "NH1" <-> "NH2" Residue "E ARG 391": "NH1" <-> "NH2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E ARG 472": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F ARG 437": "NH1" <-> "NH2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F ARG 531": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 628": "NH1" <-> "NH2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G ARG 282": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G ARG 365": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18118 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5313 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 20, 'TRANS': 635} Chain breaks: 3 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "E" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4179 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 24, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 169 Chain: "F" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1919 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain breaks: 3 Chain: "G" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3238 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain: "H" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 235 Unusual residues: {' MG': 1, 'EGY': 2, 'KZB': 3, 'KZE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'KZE:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EGY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {' MG': 1, 'EGY': 1, 'KZB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'EGY': 1, 'KZB': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'KZB': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.61, per 1000 atoms: 0.53 Number of scatterers: 18118 At special positions: 0 Unit cell: (106.68, 147.84, 183.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 8 15.00 Mg 2 11.99 O 3325 8.00 N 2826 7.00 C 11889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA K 3 " - " MAN K 6 " " MAN K 6 " - " MAN K 8 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG J 1 " - " ASN A 548 " " NAG K 1 " - " ASN E 299 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.2 seconds 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 14 sheets defined 41.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 11 through 34 Processing helix chain 'A' and resid 37 through 40 No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 119 through 138 removed outlier: 3.736A pdb=" N THR A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.851A pdb=" N PHE A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 208 Processing helix chain 'A' and resid 210 through 217 removed outlier: 4.165A pdb=" N VAL A 213 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.548A pdb=" N LEU A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.749A pdb=" N SER A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 331 through 334 No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 368 through 380 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 405 through 429 removed outlier: 3.891A pdb=" N LEU A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.794A pdb=" N CYS A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 481 Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 596 through 605 removed outlier: 4.248A pdb=" N SER A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 638 through 641 No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.698A pdb=" N ILE B 9 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 42 Proline residue: C 19 - end of helix removed outlier: 3.908A pdb=" N VAL C 23 " --> pdb=" O HIS C 20 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 24 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 25 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE C 28 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 50 through 75 Processing helix chain 'D' and resid 7 through 18 removed outlier: 3.662A pdb=" N LEU D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 48 Processing helix chain 'D' and resid 53 through 77 removed outlier: 3.599A pdb=" N CYS D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 90 through 111 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 338 through 341 No H-bonds generated for 'chain 'E' and resid 338 through 341' Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 432 through 458 removed outlier: 3.776A pdb=" N MET E 435 " --> pdb=" O LYS E 432 " (cutoff:3.500A) Proline residue: E 439 - end of helix Processing helix chain 'E' and resid 467 through 500 removed outlier: 3.654A pdb=" N ARG E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE E 478 " --> pdb=" O LYS E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 Processing helix chain 'E' and resid 541 through 564 Processing helix chain 'E' and resid 573 through 592 Processing helix chain 'F' and resid 539 through 563 Proline residue: F 552 - end of helix Processing helix chain 'F' and resid 574 through 595 removed outlier: 3.773A pdb=" N TRP F 594 " --> pdb=" O MET F 590 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 595 " --> pdb=" O TYR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 628 Processing helix chain 'G' and resid 54 through 59 removed outlier: 3.589A pdb=" N THR G 59 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 136 through 143 Processing helix chain 'G' and resid 261 through 264 Processing helix chain 'G' and resid 266 through 269 No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 288 through 299 Processing helix chain 'G' and resid 423 through 445 Proline residue: G 427 - end of helix removed outlier: 4.377A pdb=" N ALA G 432 " --> pdb=" O TYR G 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 84 through 108 removed outlier: 3.537A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 142 removed outlier: 3.731A pdb=" N LEU H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 577 through 581 removed outlier: 5.936A pdb=" N LYS A 693 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU A 680 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.650A pdb=" N HIS E 83 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR E 136 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU E 81 " --> pdb=" O THR E 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 48 through 53 removed outlier: 4.045A pdb=" N LYS E 37 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR E 170 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG E 38 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR E 172 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL E 40 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG E 174 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 68 through 71 removed outlier: 4.518A pdb=" N GLU E 95 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 153 through 158 Processing sheet with id= F, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.681A pdb=" N GLU E 395 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR E 369 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET E 230 " --> pdb=" O THR E 369 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS E 371 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 232 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE E 373 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 234 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP E 249 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET E 230 " --> pdb=" O ASN E 247 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN E 247 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG E 232 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU E 245 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE E 234 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA E 243 " --> pdb=" O ILE E 234 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 280 through 284 Processing sheet with id= H, first strand: chain 'E' and resid 342 through 345 removed outlier: 3.787A pdb=" N VAL E 425 " --> pdb=" O ASP E 384 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 374 through 376 Processing sheet with id= J, first strand: chain 'F' and resid 446 through 450 removed outlier: 3.843A pdb=" N LEU F 481 " --> pdb=" O ALA F 499 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA F 499 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA F 402 " --> pdb=" O ASP F 500 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N VAL F 502 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 12.690A pdb=" N GLY F 404 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 73 through 78 removed outlier: 3.552A pdb=" N THR G 75 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN G 96 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU G 50 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE G 98 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER G 125 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE G 99 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU G 127 " --> pdb=" O ILE G 99 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= M, first strand: chain 'G' and resid 312 through 315 Processing sheet with id= N, first strand: chain 'G' and resid 402 through 410 removed outlier: 3.604A pdb=" N LEU G 402 " --> pdb=" O TYR G 394 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY G 386 " --> pdb=" O VAL G 410 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP G 393 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN G 354 " --> pdb=" O ASP G 393 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2739 1.30 - 1.43: 4981 1.43 - 1.56: 10654 1.56 - 1.68: 91 1.68 - 1.81: 119 Bond restraints: 18584 Sorted by residual: bond pdb=" C03 KZB E 710 " pdb=" C04 KZB E 710 " ideal model delta sigma weight residual 2.203 1.521 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB A 812 " pdb=" C04 KZB A 812 " ideal model delta sigma weight residual 2.203 1.522 0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB A 814 " pdb=" C04 KZB A 814 " ideal model delta sigma weight residual 2.203 1.522 0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB G 501 " pdb=" C04 KZB G 501 " ideal model delta sigma weight residual 2.203 1.523 0.680 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB E 709 " pdb=" C04 KZB E 709 " ideal model delta sigma weight residual 2.203 1.523 0.680 2.00e-02 2.50e+03 1.16e+03 ... (remaining 18579 not shown) Histogram of bond angle deviations from ideal: 97.28 - 105.35: 428 105.35 - 113.41: 10757 113.41 - 121.48: 10152 121.48 - 129.55: 3879 129.55 - 137.61: 114 Bond angle restraints: 25330 Sorted by residual: angle pdb=" C14 KZE A 818 " pdb=" C13 KZE A 818 " pdb=" C16 KZE A 818 " ideal model delta sigma weight residual 68.20 119.83 -51.63 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C24 KZE A 818 " pdb=" C22 KZE A 818 " pdb=" C26 KZE A 818 " ideal model delta sigma weight residual 68.20 119.42 -51.22 3.00e+00 1.11e-01 2.91e+02 angle pdb=" C TYR A 89 " pdb=" N PRO A 90 " pdb=" CA PRO A 90 " ideal model delta sigma weight residual 120.83 137.61 -16.78 1.02e+00 9.61e-01 2.71e+02 angle pdb=" C21 KZE A 818 " pdb=" C22 KZE A 818 " pdb=" C26 KZE A 818 " ideal model delta sigma weight residual 85.84 119.97 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C12 KZE A 818 " pdb=" C13 KZE A 818 " pdb=" C16 KZE A 818 " ideal model delta sigma weight residual 85.84 119.83 -33.99 3.00e+00 1.11e-01 1.28e+02 ... (remaining 25325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 10982 33.86 - 67.71: 192 67.71 - 101.57: 54 101.57 - 135.43: 18 135.43 - 169.28: 2 Dihedral angle restraints: 11248 sinusoidal: 4816 harmonic: 6432 Sorted by residual: dihedral pdb=" CA THR A 606 " pdb=" C THR A 606 " pdb=" N ASP A 607 " pdb=" CA ASP A 607 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" C33 EGY D 701 " pdb=" C31 EGY D 701 " pdb=" C32 EGY D 701 " pdb=" O31 EGY D 701 " ideal model delta sinusoidal sigma weight residual 182.02 12.74 169.28 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C33 EGY C 102 " pdb=" C31 EGY C 102 " pdb=" C32 EGY C 102 " pdb=" O31 EGY C 102 " ideal model delta sinusoidal sigma weight residual 182.02 42.82 139.20 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 11245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 2991 0.965 - 1.929: 0 1.929 - 2.894: 0 2.894 - 3.859: 0 3.859 - 4.823: 2 Chirality restraints: 2993 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-02 2.50e+03 1.59e+03 chirality pdb=" C1 MAN J 7 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 7 " pdb=" O5 MAN J 7 " both_signs ideal model delta sigma weight residual False 2.40 1.77 0.63 2.00e-02 2.50e+03 9.99e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.64e+02 ... (remaining 2990 not shown) Planarity restraints: 3047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 154 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 155 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 424 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ASN F 424 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN F 424 " -0.012 2.00e-02 2.50e+03 pdb=" N THR F 425 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 416 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE A 416 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE A 416 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 417 " 0.010 2.00e-02 2.50e+03 ... (remaining 3044 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3123 2.77 - 3.30: 17352 3.30 - 3.83: 28456 3.83 - 4.37: 32510 4.37 - 4.90: 57258 Nonbonded interactions: 138699 Sorted by model distance: nonbonded pdb=" OG SER A 358 " pdb=" O VAL H 79 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP G 158 " pdb=" CG2 THR G 220 " model vdw 2.236 3.460 nonbonded pdb=" N ASP A 696 " pdb=" OD1 ASP A 696 " model vdw 2.261 2.520 nonbonded pdb=" OG1 THR E 168 " pdb=" NE2 GLN E 171 " model vdw 2.264 2.520 nonbonded pdb=" O VAL E 300 " pdb=" O6 NAG K 1 " model vdw 2.266 2.440 ... (remaining 138694 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 'J' selection = chain 'K' } 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 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 13.510 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 48.130 Find NCS groups from input model: 0.520 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.032 0.682 18584 Z= 1.899 Angle : 1.271 51.628 25330 Z= 0.576 Chirality : 0.154 4.823 2993 Planarity : 0.005 0.072 3045 Dihedral : 15.390 169.285 7110 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.68 % Favored : 94.13 % Rotamer: Outliers : 1.47 % Allowed : 7.57 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2165 helix: 0.25 (0.16), residues: 960 sheet: -0.86 (0.28), residues: 315 loop : -2.77 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 526 HIS 0.004 0.001 HIS E 160 PHE 0.018 0.002 PHE G 263 TYR 0.017 0.001 TYR E 292 ARG 0.006 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 343 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8738 (tmm) cc_final: 0.8367 (tpt) REVERT: A 329 ARG cc_start: 0.7477 (ptt-90) cc_final: 0.7027 (ttm-80) REVERT: A 485 SER cc_start: 0.8108 (t) cc_final: 0.7841 (p) REVERT: D 31 LEU cc_start: 0.8717 (tt) cc_final: 0.8371 (mp) REVERT: E 344 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.7813 (p0) REVERT: F 494 ILE cc_start: 0.8236 (pt) cc_final: 0.7961 (pt) REVERT: F 589 LEU cc_start: 0.8435 (tt) cc_final: 0.8233 (tp) REVERT: G 262 ASP cc_start: 0.7261 (m-30) cc_final: 0.6958 (m-30) outliers start: 27 outliers final: 8 residues processed: 364 average time/residue: 0.2922 time to fit residues: 161.4634 Evaluate side-chains 196 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 114 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 170 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 217 ASN A 424 GLN A 514 HIS A 515 ASN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 594 ASN A 665 ASN D 81 ASN E 45 HIS E 238 HIS E 267 GLN F 419 GLN F 457 ASN G 53 ASN G 159 HIS G 208 ASN G 342 ASN H 111 ASN H 116 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18584 Z= 0.258 Angle : 0.704 13.220 25330 Z= 0.326 Chirality : 0.047 0.530 2993 Planarity : 0.004 0.040 3045 Dihedral : 14.943 168.815 3293 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 4.20 % Allowed : 11.83 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2165 helix: 1.37 (0.17), residues: 940 sheet: -0.45 (0.28), residues: 312 loop : -2.26 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 496 HIS 0.005 0.001 HIS E 420 PHE 0.018 0.002 PHE G 263 TYR 0.020 0.002 TYR A 204 ARG 0.007 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 197 time to evaluate : 2.266 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8858 (mp) REVERT: A 329 ARG cc_start: 0.7660 (ptt-90) cc_final: 0.7159 (ttm-80) REVERT: A 502 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8107 (p90) REVERT: D 31 LEU cc_start: 0.8729 (tt) cc_final: 0.8391 (mp) REVERT: G 74 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (mp) REVERT: H 140 ARG cc_start: 0.8301 (tpp80) cc_final: 0.8003 (ttp80) outliers start: 77 outliers final: 43 residues processed: 255 average time/residue: 0.2919 time to fit residues: 115.2507 Evaluate side-chains 206 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 676 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 497 ASN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 329 HIS ** E 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 314 HIS G 401 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18584 Z= 0.239 Angle : 0.629 10.697 25330 Z= 0.298 Chirality : 0.044 0.489 2993 Planarity : 0.004 0.043 3045 Dihedral : 13.710 154.575 3290 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 4.52 % Allowed : 13.90 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2165 helix: 1.81 (0.17), residues: 931 sheet: -0.43 (0.27), residues: 326 loop : -2.03 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 496 HIS 0.006 0.001 HIS G 235 PHE 0.020 0.002 PHE G 149 TYR 0.026 0.001 TYR H 50 ARG 0.006 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 173 time to evaluate : 2.297 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7764 (ptt-90) cc_final: 0.7213 (ttm-80) REVERT: A 502 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8081 (p90) REVERT: D 31 LEU cc_start: 0.8768 (tt) cc_final: 0.8442 (mp) REVERT: E 32 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7616 (pt) REVERT: E 313 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7224 (mm-30) REVERT: F 590 MET cc_start: 0.8930 (tpp) cc_final: 0.8716 (tpp) REVERT: G 235 HIS cc_start: 0.7656 (t-170) cc_final: 0.7270 (t-170) REVERT: H 134 MET cc_start: 0.8095 (mmm) cc_final: 0.7895 (mmp) outliers start: 83 outliers final: 48 residues processed: 240 average time/residue: 0.3031 time to fit residues: 111.7123 Evaluate side-chains 213 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 132 optimal weight: 50.0000 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 HIS G 414 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18584 Z= 0.219 Angle : 0.601 9.941 25330 Z= 0.285 Chirality : 0.043 0.427 2993 Planarity : 0.004 0.044 3045 Dihedral : 13.004 130.638 3290 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.27 % Rotamer: Outliers : 4.31 % Allowed : 14.22 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2165 helix: 1.87 (0.17), residues: 938 sheet: -0.37 (0.27), residues: 330 loop : -1.99 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 496 HIS 0.004 0.001 HIS G 235 PHE 0.016 0.001 PHE G 263 TYR 0.017 0.001 TYR A 54 ARG 0.005 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 165 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 329 ARG cc_start: 0.7822 (ptt-90) cc_final: 0.7200 (ttm-80) REVERT: A 502 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8141 (p90) REVERT: D 31 LEU cc_start: 0.8716 (tt) cc_final: 0.8414 (mp) REVERT: E 32 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7808 (pt) REVERT: E 313 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7246 (mm-30) REVERT: F 429 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6952 (pp) REVERT: F 494 ILE cc_start: 0.8297 (pt) cc_final: 0.8082 (mt) REVERT: G 235 HIS cc_start: 0.7615 (t-170) cc_final: 0.7178 (t-170) REVERT: H 85 MET cc_start: 0.6666 (mmm) cc_final: 0.6181 (tpp) REVERT: H 106 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6782 (ttm-80) outliers start: 79 outliers final: 50 residues processed: 230 average time/residue: 0.2990 time to fit residues: 105.5063 Evaluate side-chains 206 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN E 57 HIS E 420 HIS G 414 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18584 Z= 0.343 Angle : 0.668 10.342 25330 Z= 0.321 Chirality : 0.046 0.424 2993 Planarity : 0.004 0.044 3045 Dihedral : 12.774 119.018 3290 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 5.07 % Allowed : 15.26 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2165 helix: 1.64 (0.17), residues: 934 sheet: -0.37 (0.28), residues: 325 loop : -1.93 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.005 0.002 HIS F 583 PHE 0.017 0.002 PHE A 48 TYR 0.019 0.002 TYR E 292 ARG 0.006 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 150 time to evaluate : 1.931 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9053 (mp) REVERT: A 329 ARG cc_start: 0.8009 (ptt-90) cc_final: 0.7210 (ttm-80) REVERT: A 502 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8110 (p90) REVERT: D 31 LEU cc_start: 0.8809 (tt) cc_final: 0.8413 (mp) REVERT: E 210 SER cc_start: 0.8873 (t) cc_final: 0.8509 (t) REVERT: E 313 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7309 (mm-30) REVERT: F 377 ASN cc_start: 0.7401 (t0) cc_final: 0.7180 (t0) REVERT: F 429 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6968 (pp) REVERT: G 235 HIS cc_start: 0.8269 (t-170) cc_final: 0.8003 (t70) REVERT: H 85 MET cc_start: 0.6800 (mmm) cc_final: 0.6270 (tpp) REVERT: H 106 ARG cc_start: 0.7014 (ttt180) cc_final: 0.6742 (ttm-80) outliers start: 93 outliers final: 67 residues processed: 225 average time/residue: 0.2896 time to fit residues: 100.1531 Evaluate side-chains 210 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 140 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 563 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 209 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS E 137 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18584 Z= 0.165 Angle : 0.572 10.145 25330 Z= 0.271 Chirality : 0.042 0.404 2993 Planarity : 0.004 0.042 3045 Dihedral : 12.141 117.566 3290 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 4.03 % Allowed : 16.40 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2165 helix: 1.91 (0.17), residues: 942 sheet: -0.25 (0.28), residues: 328 loop : -1.83 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 496 HIS 0.004 0.001 HIS G 235 PHE 0.016 0.001 PHE H 122 TYR 0.014 0.001 TYR A 54 ARG 0.005 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 169 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8720 (tp) REVERT: A 329 ARG cc_start: 0.7973 (ptt-90) cc_final: 0.7160 (ttm-80) REVERT: A 414 MET cc_start: 0.7849 (mmm) cc_final: 0.7622 (mmt) REVERT: A 502 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8150 (p90) REVERT: B 2 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8188 (mt) REVERT: D 31 LEU cc_start: 0.8685 (tt) cc_final: 0.8399 (mp) REVERT: E 92 ASP cc_start: 0.7465 (t0) cc_final: 0.6820 (m-30) REVERT: E 313 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7232 (mm-30) REVERT: F 377 ASN cc_start: 0.7225 (t0) cc_final: 0.7019 (t0) REVERT: F 429 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6898 (pp) REVERT: G 235 HIS cc_start: 0.7950 (t-170) cc_final: 0.7607 (t70) REVERT: H 106 ARG cc_start: 0.7059 (ttt180) cc_final: 0.6788 (ttm-80) outliers start: 74 outliers final: 48 residues processed: 229 average time/residue: 0.2941 time to fit residues: 104.4106 Evaluate side-chains 203 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18584 Z= 0.165 Angle : 0.565 9.749 25330 Z= 0.266 Chirality : 0.042 0.391 2993 Planarity : 0.004 0.041 3045 Dihedral : 11.684 116.638 3285 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 3.71 % Allowed : 17.17 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 2165 helix: 2.03 (0.17), residues: 939 sheet: -0.13 (0.28), residues: 328 loop : -1.78 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 496 HIS 0.003 0.001 HIS G 235 PHE 0.015 0.001 PHE G 263 TYR 0.017 0.001 TYR A 54 ARG 0.003 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 329 ARG cc_start: 0.7978 (ptt-90) cc_final: 0.7147 (ttm-80) REVERT: A 502 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8169 (p90) REVERT: B 2 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8136 (mt) REVERT: D 31 LEU cc_start: 0.8642 (tt) cc_final: 0.8384 (mt) REVERT: E 92 ASP cc_start: 0.7362 (t0) cc_final: 0.6811 (m-30) REVERT: E 210 SER cc_start: 0.8703 (t) cc_final: 0.8413 (t) REVERT: E 313 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7221 (mm-30) REVERT: F 429 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6898 (pp) REVERT: G 235 HIS cc_start: 0.7878 (t-170) cc_final: 0.7531 (t70) REVERT: H 106 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6756 (ttm-80) REVERT: H 138 PHE cc_start: 0.8489 (m-80) cc_final: 0.8276 (m-80) outliers start: 68 outliers final: 51 residues processed: 218 average time/residue: 0.2922 time to fit residues: 98.3146 Evaluate side-chains 207 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18584 Z= 0.312 Angle : 0.628 9.845 25330 Z= 0.302 Chirality : 0.044 0.382 2993 Planarity : 0.004 0.044 3045 Dihedral : 11.761 117.267 3285 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 3.92 % Allowed : 16.89 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2165 helix: 1.86 (0.17), residues: 929 sheet: -0.21 (0.28), residues: 327 loop : -1.79 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 525 HIS 0.004 0.001 HIS F 583 PHE 0.023 0.002 PHE H 122 TYR 0.017 0.001 TYR E 292 ARG 0.004 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 148 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8824 (tp) REVERT: A 329 ARG cc_start: 0.8084 (ptt-90) cc_final: 0.7195 (ttm-80) REVERT: A 502 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8120 (p90) REVERT: D 31 LEU cc_start: 0.8818 (tt) cc_final: 0.8459 (mp) REVERT: E 210 SER cc_start: 0.8835 (t) cc_final: 0.8515 (t) REVERT: E 313 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7291 (mm-30) REVERT: F 429 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6816 (pp) REVERT: H 85 MET cc_start: 0.6662 (mmm) cc_final: 0.6259 (tpp) REVERT: H 106 ARG cc_start: 0.7125 (ttt180) cc_final: 0.6818 (ttm-80) outliers start: 72 outliers final: 59 residues processed: 208 average time/residue: 0.3051 time to fit residues: 96.7364 Evaluate side-chains 201 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 0.0770 chunk 182 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18584 Z= 0.157 Angle : 0.559 9.660 25330 Z= 0.266 Chirality : 0.042 0.384 2993 Planarity : 0.004 0.043 3045 Dihedral : 11.388 115.750 3285 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 3.32 % Allowed : 17.38 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2165 helix: 2.06 (0.17), residues: 936 sheet: -0.07 (0.28), residues: 334 loop : -1.71 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 496 HIS 0.003 0.001 HIS G 235 PHE 0.022 0.001 PHE H 122 TYR 0.019 0.001 TYR A 54 ARG 0.009 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 1.965 Fit side-chains REVERT: A 226 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 329 ARG cc_start: 0.8042 (ptt-90) cc_final: 0.7218 (ttm-80) REVERT: A 502 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8162 (p90) REVERT: B 2 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8060 (mt) REVERT: D 31 LEU cc_start: 0.8641 (tt) cc_final: 0.8374 (mp) REVERT: E 210 SER cc_start: 0.8747 (t) cc_final: 0.8451 (t) REVERT: E 313 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7166 (mm-30) REVERT: F 429 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6817 (pp) REVERT: G 235 HIS cc_start: 0.7857 (t-170) cc_final: 0.7501 (t70) REVERT: H 106 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6792 (ttm-80) REVERT: H 138 PHE cc_start: 0.8491 (m-80) cc_final: 0.8289 (m-80) outliers start: 61 outliers final: 48 residues processed: 213 average time/residue: 0.2991 time to fit residues: 97.6195 Evaluate side-chains 202 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18584 Z= 0.277 Angle : 0.612 9.527 25330 Z= 0.293 Chirality : 0.044 0.374 2993 Planarity : 0.004 0.043 3045 Dihedral : 11.422 116.677 3285 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 3.43 % Allowed : 17.60 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2165 helix: 1.93 (0.17), residues: 936 sheet: -0.12 (0.28), residues: 333 loop : -1.80 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 74 HIS 0.004 0.001 HIS F 583 PHE 0.017 0.001 PHE G 263 TYR 0.018 0.001 TYR A 54 ARG 0.008 0.000 ARG F 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4330 Ramachandran restraints generated. 2165 Oldfield, 0 Emsley, 2165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 150 time to evaluate : 2.191 Fit side-chains REVERT: A 226 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 329 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.7261 (ttm-80) REVERT: A 502 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8085 (p90) REVERT: B 2 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8040 (mt) REVERT: D 31 LEU cc_start: 0.8763 (tt) cc_final: 0.8469 (mp) REVERT: E 210 SER cc_start: 0.8863 (t) cc_final: 0.8568 (t) REVERT: E 313 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7261 (mm-30) REVERT: F 429 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6877 (pp) REVERT: G 235 HIS cc_start: 0.8069 (t-170) cc_final: 0.7724 (t70) outliers start: 63 outliers final: 56 residues processed: 204 average time/residue: 0.3058 time to fit residues: 95.5131 Evaluate side-chains 204 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 144 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 472 ARG Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 chunk 177 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093043 restraints weight = 28639.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096190 restraints weight = 14750.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098240 restraints weight = 9707.602| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18584 Z= 0.160 Angle : 0.561 9.911 25330 Z= 0.267 Chirality : 0.042 0.375 2993 Planarity : 0.004 0.043 3045 Dihedral : 11.090 115.069 3285 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 3.38 % Allowed : 17.71 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2165 helix: 2.06 (0.17), residues: 934 sheet: -0.04 (0.28), residues: 334 loop : -1.70 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 496 HIS 0.003 0.001 HIS G 235 PHE 0.021 0.001 PHE H 122 TYR 0.018 0.001 TYR A 54 ARG 0.008 0.000 ARG F 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.84 seconds wall clock time: 67 minutes 4.70 seconds (4024.70 seconds total)