Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 08:26:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6g_21554/04_2023/6w6g_21554_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 67 5.16 5 C 17109 2.51 5 N 5033 2.21 5 O 5338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A ASP 635": "OD1" <-> "OD2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 626": "OD1" <-> "OD2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B ASP 635": "OD1" <-> "OD2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 729": "OE1" <-> "OE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B ASP 841": "OD1" <-> "OD2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 532": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ASP 584": "OD1" <-> "OD2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 626": "OD1" <-> "OD2" Residue "C TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 766": "OD1" <-> "OD2" Residue "C ASP 832": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 531": "OE1" <-> "OE2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D ASP 635": "OD1" <-> "OD2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 766": "OD1" <-> "OD2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D ASP 841": "OD1" <-> "OD2" Residue "D ASP 843": "OD1" <-> "OD2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E ASP 356": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "E ASP 536": "OD1" <-> "OD2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 622": "OD1" <-> "OD2" Residue "E GLU 628": "OE1" <-> "OE2" Residue "E ASP 635": "OD1" <-> "OD2" Residue "E TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 679": "OD1" <-> "OD2" Residue "E ASP 690": "OD1" <-> "OD2" Residue "E ASP 697": "OD1" <-> "OD2" Residue "E GLU 698": "OE1" <-> "OE2" Residue "E GLU 754": "OE1" <-> "OE2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "E ASP 817": "OD1" <-> "OD2" Residue "E ASP 841": "OD1" <-> "OD2" Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ASP 178": "OD1" <-> "OD2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ASP 227": "OD1" <-> "OD2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F ASP 278": "OD1" <-> "OD2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F ASP 536": "OD1" <-> "OD2" Residue "F ASP 540": "OD1" <-> "OD2" Residue "F ARG 590": "NH1" <-> "NH2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 626": "OD1" <-> "OD2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F ASP 635": "OD1" <-> "OD2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F ASP 687": "OD1" <-> "OD2" Residue "F ASP 697": "OD1" <-> "OD2" Residue "F ASP 703": "OD1" <-> "OD2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F ARG 796": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27581 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4796 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 24, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4115 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 21, 'TRANS': 509} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.85, per 1000 atoms: 0.50 Number of scatterers: 27581 At special positions: 0 Unit cell: (137.472, 147.138, 135.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 34 15.00 O 5338 8.00 N 5033 7.00 C 17109 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.09 Conformation dependent library (CDL) restraints added in 4.6 seconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 23 sheets defined 44.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.736A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.580A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 344 through 361 removed outlier: 5.035A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.928A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.650A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 437 through 468 removed outlier: 4.147A pdb=" N LEU A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 443 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 444 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 446 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 454 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 463 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.614A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.515A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 623 removed outlier: 3.792A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.509A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 689 through 695 removed outlier: 4.523A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 741 through 744 No H-bonds generated for 'chain 'A' and resid 741 through 744' Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 805 through 825 removed outlier: 4.594A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.505A pdb=" N ILE B 283 " --> pdb=" O LEU B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.837A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 344 through 361 removed outlier: 3.887A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 380 removed outlier: 3.566A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.586A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.684A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 468 removed outlier: 3.803A pdb=" N LEU B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 576 through 590 removed outlier: 4.118A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.896A pdb=" N ALA B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 removed outlier: 3.725A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 668 No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 732 through 738 removed outlier: 4.039A pdb=" N ALA B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 762 through 779 removed outlier: 3.813A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG B 779 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.946A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'C' and resid 161 through 164 No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.711A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 306' Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.692A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 368 through 380 removed outlier: 4.133A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 380 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 392 through 406 Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.555A pdb=" N ARG C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 468 removed outlier: 3.908A pdb=" N ALA C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 464 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 558 through 570 removed outlier: 5.807A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 3.723A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.936A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'C' and resid 690 through 697 removed outlier: 4.552A pdb=" N GLN C 694 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 696 " --> pdb=" O LEU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 738 removed outlier: 3.744A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 779 removed outlier: 3.970A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 3.777A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 823 removed outlier: 4.714A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 193 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.656A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.972A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.928A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 333' Processing helix chain 'D' and resid 344 through 361 removed outlier: 5.188A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 4.206A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.786A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 558 through 562 Processing helix chain 'D' and resid 576 through 590 removed outlier: 3.707A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 642 through 647 removed outlier: 3.766A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 692 through 695 No H-bonds generated for 'chain 'D' and resid 692 through 695' Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 741 through 744 No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 761 through 775 Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 805 through 824 removed outlier: 4.220A pdb=" N ARG D 808 " --> pdb=" O ARG D 805 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG D 809 " --> pdb=" O PRO D 806 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY D 816 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP D 817 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D 818 " --> pdb=" O ILE D 815 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 821 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET D 822 " --> pdb=" O LEU D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.747A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 242 through 245 No H-bonds generated for 'chain 'E' and resid 242 through 245' Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 298 through 306 Proline residue: E 302 - end of helix removed outlier: 3.635A pdb=" N ARG E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 4.051A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 3.612A pdb=" N ASP E 540 " --> pdb=" O ASP E 536 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 613 through 624 removed outlier: 4.029A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 648 No H-bonds generated for 'chain 'E' and resid 646 through 648' Processing helix chain 'E' and resid 665 through 669 Processing helix chain 'E' and resid 681 through 683 No H-bonds generated for 'chain 'E' and resid 681 through 683' Processing helix chain 'E' and resid 688 through 694 Processing helix chain 'E' and resid 731 through 738 Processing helix chain 'E' and resid 741 through 746 removed outlier: 3.536A pdb=" N ASN E 745 " --> pdb=" O PRO E 741 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 746 " --> pdb=" O GLU E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 746' Processing helix chain 'E' and resid 759 through 774 removed outlier: 3.896A pdb=" N VAL E 762 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG E 763 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 774 " --> pdb=" O GLN E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 798 removed outlier: 4.179A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 825 removed outlier: 3.875A pdb=" N ARG E 808 " --> pdb=" O ARG E 805 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 810 " --> pdb=" O LEU E 807 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 815 " --> pdb=" O GLN E 812 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 816 " --> pdb=" O GLN E 813 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 817 " --> pdb=" O ALA E 814 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS E 821 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 823 " --> pdb=" O ALA E 820 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.605A pdb=" N LYS F 163 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.533A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 344 through 353 removed outlier: 4.456A pdb=" N ARG F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY F 353 " --> pdb=" O GLY F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 377 removed outlier: 4.164A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 405 Processing helix chain 'F' and resid 535 through 543 Processing helix chain 'F' and resid 568 through 571 No H-bonds generated for 'chain 'F' and resid 568 through 571' Processing helix chain 'F' and resid 576 through 589 Processing helix chain 'F' and resid 613 through 619 Processing helix chain 'F' and resid 621 through 624 No H-bonds generated for 'chain 'F' and resid 621 through 624' Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.694A pdb=" N ASP F 690 " --> pdb=" O PRO F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 Processing helix chain 'F' and resid 758 through 779 removed outlier: 3.879A pdb=" N LEU F 761 " --> pdb=" O PRO F 758 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL F 762 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG F 763 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 777 " --> pdb=" O LYS F 774 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN F 778 " --> pdb=" O ARG F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 796 removed outlier: 3.914A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG F 796 " --> pdb=" O TRP F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 804 through 824 removed outlier: 4.042A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.831A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY A 206 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 315 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 314 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 602 through 606 removed outlier: 6.633A pdb=" N LEU A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE A 605 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU A 718 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 700 through 702 Processing sheet with id= D, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.947A pdb=" N VAL A 834 " --> pdb=" O GLN A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.112A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG B 310 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 277 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 312 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 206 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 335 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE B 205 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 337 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 750 through 752 removed outlier: 8.906A pdb=" N LEU B 751 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET B 604 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 718 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 720 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 165 through 167 removed outlier: 3.714A pdb=" N ALA C 239 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 339 removed outlier: 6.578A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLY C 206 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 315 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 750 through 752 removed outlier: 8.010A pdb=" N LEU C 751 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N MET C 604 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 716 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE C 605 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 718 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 700 through 702 Processing sheet with id= K, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.137A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 165 through 167 removed outlier: 4.867A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 312 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 206 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN D 335 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE D 205 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL D 337 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 604 through 606 Processing sheet with id= N, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.157A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 782 through 785 removed outlier: 4.283A pdb=" N VAL D 836 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.519A pdb=" N GLY E 313 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.939A pdb=" N ILE E 274 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU E 240 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE E 276 " --> pdb=" O LEU E 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 601 through 604 removed outlier: 3.655A pdb=" N PHE E 603 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 718 " --> pdb=" O PHE E 603 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 700 through 702 Processing sheet with id= T, first strand: chain 'F' and resid 313 through 316 Processing sheet with id= U, first strand: chain 'F' and resid 602 through 606 removed outlier: 6.019A pdb=" N LEU F 716 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE F 605 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU F 718 " --> pdb=" O PHE F 605 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 631 through 634 removed outlier: 5.862A pdb=" N VAL F 675 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE F 634 " --> pdb=" O VAL F 675 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F 677 " --> pdb=" O ILE F 634 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 782 through 784 855 hydrogen bonds defined for protein. 2316 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: 8.49 Time building geometry restraints manager: 11.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 9771 1.37 - 1.51: 8222 1.51 - 1.66: 9836 1.66 - 1.80: 110 1.80 - 1.95: 14 Bond restraints: 27953 Sorted by residual: bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP E 902 " pdb=" C6 ADP E 902 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CA ALA B 621 " pdb=" C ALA B 621 " ideal model delta sigma weight residual 1.522 1.474 0.048 1.38e-02 5.25e+03 1.22e+01 bond pdb=" CA ALA A 621 " pdb=" C ALA A 621 " ideal model delta sigma weight residual 1.523 1.480 0.044 1.80e-02 3.09e+03 5.85e+00 bond pdb=" CA THR A 600 " pdb=" C THR A 600 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.80e-02 3.09e+03 5.32e+00 ... (remaining 27948 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.95: 821 106.95 - 114.25: 16488 114.25 - 121.56: 14002 121.56 - 128.86: 6371 128.86 - 136.16: 127 Bond angle restraints: 37809 Sorted by residual: angle pdb=" N ILE A 413 " pdb=" CA ILE A 413 " pdb=" C ILE A 413 " ideal model delta sigma weight residual 111.90 106.25 5.65 8.10e-01 1.52e+00 4.87e+01 angle pdb=" N ASN B 298 " pdb=" CA ASN B 298 " pdb=" C ASN B 298 " ideal model delta sigma weight residual 114.39 107.20 7.19 1.45e+00 4.76e-01 2.46e+01 angle pdb=" N VAL F 210 " pdb=" CA VAL F 210 " pdb=" C VAL F 210 " ideal model delta sigma weight residual 113.71 109.06 4.65 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N VAL A 593 " pdb=" CA VAL A 593 " pdb=" C VAL A 593 " ideal model delta sigma weight residual 113.53 109.32 4.21 9.80e-01 1.04e+00 1.84e+01 angle pdb=" C ASN D 597 " pdb=" N ARG D 598 " pdb=" CA ARG D 598 " ideal model delta sigma weight residual 121.80 131.89 -10.09 2.44e+00 1.68e-01 1.71e+01 ... (remaining 37804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 16616 32.78 - 65.56: 499 65.56 - 98.33: 34 98.33 - 131.11: 2 131.11 - 163.89: 2 Dihedral angle restraints: 17153 sinusoidal: 7093 harmonic: 10060 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -116.09 -63.91 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PHE C 386 " pdb=" C PHE C 386 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " ideal model delta harmonic sigma weight residual 180.00 -143.81 -36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" O2A ADP E 902 " pdb=" O3A ADP E 902 " pdb=" PA ADP E 902 " pdb=" PB ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 136.11 163.89 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 17150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2643 0.037 - 0.074: 1209 0.074 - 0.111: 364 0.111 - 0.148: 102 0.148 - 0.185: 10 Chirality restraints: 4328 Sorted by residual: chirality pdb=" CB ILE F 273 " pdb=" CA ILE F 273 " pdb=" CG1 ILE F 273 " pdb=" CG2 ILE F 273 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA LEU C 387 " pdb=" N LEU C 387 " pdb=" C LEU C 387 " pdb=" CB LEU C 387 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" PA AGS A 902 " pdb=" O2A AGS A 902 " pdb=" O3A AGS A 902 " pdb=" O5' AGS A 902 " both_signs ideal model delta sigma weight residual True 3.18 -3.02 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 4325 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 388 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 545 " -0.021 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 545 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 545 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 545 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 545 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 545 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 545 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 545 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 545 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 545 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 652 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO E 653 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 653 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 653 " 0.032 5.00e-02 4.00e+02 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 713 2.68 - 3.24: 27497 3.24 - 3.79: 39745 3.79 - 4.35: 54488 4.35 - 4.90: 90330 Nonbonded interactions: 212773 Sorted by model distance: nonbonded pdb=" O1B AGS B 902 " pdb=" O2G AGS B 902 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR E 639 " pdb=" OE1 GLN E 663 " model vdw 2.132 2.440 nonbonded pdb=" O1B AGS A 901 " pdb=" O2G AGS A 901 " model vdw 2.150 2.440 nonbonded pdb=" O1B AGS D 902 " pdb=" O2G AGS D 902 " model vdw 2.168 2.440 nonbonded pdb=" O THR C 236 " pdb=" OG1 THR C 236 " model vdw 2.173 2.440 ... (remaining 212768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 650 or resid 663 through 845 or resid 901)) selection = (chain 'F' and (resid 159 through 845 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.730 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 68.360 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.006 0.109 27953 Z= 0.365 Angle : 0.787 12.116 37809 Z= 0.450 Chirality : 0.046 0.185 4328 Planarity : 0.005 0.101 4946 Dihedral : 15.447 163.888 10665 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.52 % Favored : 88.31 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -4.32 (0.12), residues: 3464 helix: -2.09 (0.11), residues: 1693 sheet: -3.21 (0.23), residues: 356 loop : -3.68 (0.13), residues: 1415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 278 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 295 average time/residue: 0.5563 time to fit residues: 235.9518 Evaluate side-chains 184 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 3.416 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 16 average time/residue: 0.2444 time to fit residues: 12.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 20.0000 chunk 266 optimal weight: 0.0020 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 336 GLN A 361 HIS B 361 HIS B 464 GLN B 468 ASN B 694 GLN B 778 GLN B 813 GLN C 643 HIS C 663 GLN C 685 HIS C 812 GLN D 643 HIS D 705 HIS D 730 GLN D 784 GLN D 827 GLN E 201 ASN E 685 HIS E 768 GLN F 201 ASN F 812 GLN F 837 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 27953 Z= 0.169 Angle : 0.617 14.925 37809 Z= 0.308 Chirality : 0.042 0.187 4328 Planarity : 0.005 0.088 4946 Dihedral : 8.624 132.442 4005 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.25 % Favored : 89.67 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.14), residues: 3464 helix: -0.93 (0.13), residues: 1673 sheet: -2.72 (0.23), residues: 372 loop : -3.03 (0.15), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 237 average time/residue: 0.4387 time to fit residues: 166.2050 Evaluate side-chains 188 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 3.608 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 28 average time/residue: 0.2658 time to fit residues: 18.9608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 319 optimal weight: 0.2980 chunk 344 optimal weight: 0.0050 chunk 284 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 256 optimal weight: 0.0010 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS A 705 HIS B 694 GLN E 768 GLN E 813 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 812 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 27953 Z= 0.144 Angle : 0.567 14.585 37809 Z= 0.280 Chirality : 0.041 0.253 4328 Planarity : 0.005 0.085 4946 Dihedral : 8.185 134.027 4005 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.05 % Favored : 89.84 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3464 helix: -0.39 (0.13), residues: 1644 sheet: -2.45 (0.24), residues: 374 loop : -2.65 (0.15), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 32 residues processed: 246 average time/residue: 0.4299 time to fit residues: 168.5243 Evaluate side-chains 198 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 3.766 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 19 residues processed: 32 average time/residue: 0.2559 time to fit residues: 20.3548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 165 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 214 optimal weight: 0.0060 chunk 320 optimal weight: 6.9990 chunk 339 optimal weight: 10.0000 chunk 167 optimal weight: 0.0870 chunk 303 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS B 201 ASN B 685 HIS B 694 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 768 GLN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 27953 Z= 0.229 Angle : 0.597 14.249 37809 Z= 0.292 Chirality : 0.043 0.210 4328 Planarity : 0.005 0.091 4946 Dihedral : 8.160 127.568 4005 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.22 % Favored : 89.69 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3464 helix: -0.23 (0.13), residues: 1639 sheet: -2.32 (0.23), residues: 385 loop : -2.48 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 170 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 39 residues processed: 225 average time/residue: 0.4088 time to fit residues: 148.8971 Evaluate side-chains 193 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 3.369 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 20 residues processed: 39 average time/residue: 0.2499 time to fit residues: 23.2585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 252 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 304 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS B 201 ASN B 694 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 829 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 730 GLN F 812 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 27953 Z= 0.260 Angle : 0.610 14.810 37809 Z= 0.299 Chirality : 0.043 0.182 4328 Planarity : 0.005 0.093 4946 Dihedral : 8.165 123.088 4005 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.48 % Favored : 89.43 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.14), residues: 3464 helix: -0.13 (0.14), residues: 1642 sheet: -2.20 (0.24), residues: 376 loop : -2.42 (0.15), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 208 average time/residue: 0.4127 time to fit residues: 140.1742 Evaluate side-chains 185 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 31 average time/residue: 0.2645 time to fit residues: 19.8269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 199 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 339 optimal weight: 0.1980 chunk 281 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 178 optimal weight: 0.2980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS B 281 HIS E 813 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 27953 Z= 0.141 Angle : 0.550 14.635 37809 Z= 0.270 Chirality : 0.041 0.185 4328 Planarity : 0.004 0.088 4946 Dihedral : 7.755 118.081 4005 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.58 % Favored : 90.33 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.67 (0.15), residues: 3464 helix: 0.07 (0.14), residues: 1651 sheet: -1.87 (0.25), residues: 375 loop : -2.30 (0.16), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 28 residues processed: 215 average time/residue: 0.4156 time to fit residues: 145.3447 Evaluate side-chains 185 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 28 average time/residue: 0.2577 time to fit residues: 18.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 285 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 338 optimal weight: 0.0060 chunk 211 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 156 optimal weight: 0.0980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS C 812 GLN E 597 ASN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.069 27953 Z= 0.146 Angle : 0.560 14.725 37809 Z= 0.269 Chirality : 0.041 0.183 4328 Planarity : 0.004 0.078 4946 Dihedral : 7.561 116.518 4005 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.44 % Favored : 90.50 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.48 (0.15), residues: 3464 helix: 0.23 (0.14), residues: 1653 sheet: -1.76 (0.25), residues: 378 loop : -2.20 (0.16), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 201 average time/residue: 0.4101 time to fit residues: 135.4983 Evaluate side-chains 180 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 3.368 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 23 average time/residue: 0.2487 time to fit residues: 15.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 268 ASN E 597 ASN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 829 HIS F 757 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 27953 Z= 0.172 Angle : 0.561 13.674 37809 Z= 0.272 Chirality : 0.042 0.181 4328 Planarity : 0.004 0.082 4946 Dihedral : 7.534 118.694 4005 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.44 % Favored : 90.47 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.37 (0.15), residues: 3464 helix: 0.35 (0.14), residues: 1646 sheet: -1.58 (0.24), residues: 396 loop : -2.21 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 191 average time/residue: 0.4117 time to fit residues: 128.5122 Evaluate side-chains 177 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 26 average time/residue: 0.2429 time to fit residues: 16.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 189 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 chunk 284 optimal weight: 0.4980 chunk 298 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 overall best weight: 1.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 27953 Z= 0.226 Angle : 0.597 13.540 37809 Z= 0.290 Chirality : 0.043 0.176 4328 Planarity : 0.004 0.086 4946 Dihedral : 7.643 122.191 4005 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.96 % Favored : 89.95 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.35 (0.15), residues: 3464 helix: 0.36 (0.14), residues: 1640 sheet: -1.60 (0.25), residues: 402 loop : -2.19 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 3.459 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 189 average time/residue: 0.4302 time to fit residues: 136.1572 Evaluate side-chains 176 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 3.459 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 24 average time/residue: 0.2876 time to fit residues: 17.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.5980 chunk 333 optimal weight: 0.9980 chunk 203 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 349 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 215 optimal weight: 0.0770 chunk 170 optimal weight: 0.0980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 468 ASN E 597 ASN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 829 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.091 27953 Z= 0.147 Angle : 0.576 15.945 37809 Z= 0.277 Chirality : 0.041 0.223 4328 Planarity : 0.004 0.080 4946 Dihedral : 7.418 123.699 4005 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.89 % Favored : 91.05 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.15 (0.15), residues: 3464 helix: 0.55 (0.14), residues: 1628 sheet: -1.53 (0.25), residues: 408 loop : -2.09 (0.16), residues: 1428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 3.421 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 22 residues processed: 192 average time/residue: 0.4085 time to fit residues: 129.0341 Evaluate side-chains 182 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 3.605 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 22 average time/residue: 0.2595 time to fit residues: 15.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN ** E 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.081356 restraints weight = 51583.915| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.74 r_work: 0.2914 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 27953 Z= 0.336 Angle : 0.668 13.654 37809 Z= 0.323 Chirality : 0.045 0.230 4328 Planarity : 0.005 0.092 4946 Dihedral : 7.787 126.222 4005 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.33 % Favored : 89.58 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % 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: -1.37 (0.15), residues: 3464 helix: 0.31 (0.14), residues: 1657 sheet: -1.53 (0.25), residues: 393 loop : -2.19 (0.16), residues: 1414 =============================================================================== Job complete usr+sys time: 4919.86 seconds wall clock time: 90 minutes 30.99 seconds (5430.99 seconds total)