Starting phenix.real_space_refine on Mon Feb 19 11:49:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wgc_21662/02_2024/6wgc_21662_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 93 5.49 5 S 114 5.16 5 C 15526 2.51 5 N 4101 2.21 5 O 4771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "9 GLU 98": "OE1" <-> "OE2" Residue "9 ASP 119": "OD1" <-> "OD2" Residue "9 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 269": "OD1" <-> "OD2" Residue "9 PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 448": "OD1" <-> "OD2" Residue "9 GLU 457": "OE1" <-> "OE2" Residue "9 PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 490": "OD1" <-> "OD2" Residue "9 PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 875": "OD1" <-> "OD2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C ASP 489": "OD1" <-> "OD2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 296": "OD1" <-> "OD2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ARG 352": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F ARG 385": "NH1" <-> "NH2" Residue "3 ARG 892": "NH1" <-> "NH2" Residue "3 ARG 902": "NH1" <-> "NH2" Residue "3 GLU 912": "OE1" <-> "OE2" Residue "3 TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 921": "OE1" <-> "OE2" Residue "3 ARG 922": "NH1" <-> "NH2" Residue "3 GLU 926": "OE1" <-> "OE2" Residue "3 GLU 937": "OE1" <-> "OE2" Residue "3 TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 947": "OD1" <-> "OD2" Residue "3 ARG 948": "NH1" <-> "NH2" Residue "7 GLU 763": "OE1" <-> "OE2" Residue "7 GLU 785": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24605 Number of models: 1 Model: "" Number of chains: 15 Chain: "9" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2976 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3386 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2663 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4505 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 529} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3425 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 400} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3551 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1315 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "3" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "7" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 831 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "9" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.08, per 1000 atoms: 0.49 Number of scatterers: 24605 At special positions: 0 Unit cell: (163.75, 127.07, 165.06, 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 114 16.00 P 93 15.00 O 4771 8.00 N 4101 7.00 C 15526 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=0, symmetry=0 Time building additional restraints: 10.94 Conformation dependent library (CDL) restraints added in 3.8 seconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 16 sheets defined 48.4% alpha, 5.4% beta 41 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 11.33 Creating SS restraints... Processing helix chain '9' and resid 60 through 64 Processing helix chain '9' and resid 85 through 91 removed outlier: 4.039A pdb=" N ASN 9 90 " --> pdb=" O GLU 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 114 through 128 removed outlier: 3.623A pdb=" N LEU 9 118 " --> pdb=" O LYS 9 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP 9 119 " --> pdb=" O THR 9 115 " (cutoff:3.500A) Processing helix chain '9' and resid 180 through 188 removed outlier: 4.137A pdb=" N PHE 9 186 " --> pdb=" O PHE 9 182 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP 9 187 " --> pdb=" O GLN 9 183 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER 9 188 " --> pdb=" O LYS 9 184 " (cutoff:3.500A) Processing helix chain '9' and resid 195 through 198 No H-bonds generated for 'chain '9' and resid 195 through 198' Processing helix chain '9' and resid 202 through 208 removed outlier: 3.946A pdb=" N GLN 9 206 " --> pdb=" O MET 9 202 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 9 207 " --> pdb=" O GLN 9 203 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 9 208 " --> pdb=" O HIS 9 204 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 202 through 208' Processing helix chain '9' and resid 225 through 229 removed outlier: 3.538A pdb=" N LEU 9 229 " --> pdb=" O ASP 9 226 " (cutoff:3.500A) Processing helix chain '9' and resid 238 through 246 Processing helix chain '9' and resid 296 through 304 Processing helix chain '9' and resid 314 through 322 Processing helix chain '9' and resid 333 through 336 No H-bonds generated for 'chain '9' and resid 333 through 336' Processing helix chain '9' and resid 338 through 347 Processing helix chain '9' and resid 388 through 398 removed outlier: 4.065A pdb=" N SER 9 395 " --> pdb=" O ALA 9 391 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS 9 396 " --> pdb=" O LYS 9 392 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE 9 397 " --> pdb=" O VAL 9 393 " (cutoff:3.500A) Processing helix chain '9' and resid 405 through 408 No H-bonds generated for 'chain '9' and resid 405 through 408' Processing helix chain '9' and resid 412 through 424 removed outlier: 3.697A pdb=" N ILE 9 422 " --> pdb=" O LEU 9 418 " (cutoff:3.500A) Processing helix chain '9' and resid 435 through 444 Processing helix chain '9' and resid 455 through 467 removed outlier: 3.512A pdb=" N CYS 9 462 " --> pdb=" O PHE 9 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR 9 463 " --> pdb=" O LEU 9 459 " (cutoff:3.500A) Processing helix chain '9' and resid 495 through 503 removed outlier: 3.943A pdb=" N ASP 9 500 " --> pdb=" O ARG 9 496 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU 9 501 " --> pdb=" O GLU 9 497 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 9 503 " --> pdb=" O TYR 9 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.687A pdb=" N GLN A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.770A pdb=" N SER A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 removed outlier: 4.083A pdb=" N VAL A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 3.861A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.592A pdb=" N MET A 543 " --> pdb=" O TRP A 539 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 577 through 584 removed outlier: 3.866A pdb=" N ASN A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 Proline residue: A 605 - end of helix No H-bonds generated for 'chain 'A' and resid 602 through 607' Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.839A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.605A pdb=" N ILE A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.644A pdb=" N LYS A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 725 removed outlier: 3.574A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 785 removed outlier: 3.599A pdb=" N LYS A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.732A pdb=" N ILE A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.676A pdb=" N ASN A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.674A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.502A pdb=" N ILE B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix removed outlier: 3.697A pdb=" N THR B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.998A pdb=" N ALA B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 removed outlier: 3.508A pdb=" N PHE B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.951A pdb=" N PHE B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 removed outlier: 3.759A pdb=" N MET B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 519 through 534 removed outlier: 3.602A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.876A pdb=" N MET B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 removed outlier: 3.882A pdb=" N GLU B 610 " --> pdb=" O TYR B 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 4.284A pdb=" N LEU C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 156 removed outlier: 3.782A pdb=" N SER C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.815A pdb=" N GLU C 189 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 191 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 194 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE C 195 " --> pdb=" O LYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.537A pdb=" N ILE C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.669A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.567A pdb=" N LEU C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.641A pdb=" N THR C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.706A pdb=" N PHE C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 331 removed outlier: 3.608A pdb=" N PHE C 330 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.847A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 3.721A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.589A pdb=" N LYS C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 386 through 395 removed outlier: 4.357A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 3.913A pdb=" N ARG C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 412 " --> pdb=" O PHE C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.507A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.713A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 557 removed outlier: 3.528A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 removed outlier: 4.129A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 587 removed outlier: 3.856A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 20 Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.583A pdb=" N LYS E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 86 removed outlier: 3.735A pdb=" N GLN E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 removed outlier: 4.221A pdb=" N VAL E 109 " --> pdb=" O PRO E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 155 removed outlier: 3.595A pdb=" N LEU E 155 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 194 through 209 removed outlier: 3.501A pdb=" N SER E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET E 203 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.539A pdb=" N VAL E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 251 No H-bonds generated for 'chain 'E' and resid 248 through 251' Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.591A pdb=" N ASP E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 326 through 339 removed outlier: 4.136A pdb=" N ILE E 337 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER E 339 " --> pdb=" O SER E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 385 through 392 removed outlier: 3.903A pdb=" N ALA E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 429 removed outlier: 3.626A pdb=" N LEU E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER E 425 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 465 removed outlier: 3.556A pdb=" N GLU E 464 " --> pdb=" O LYS E 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 removed outlier: 3.567A pdb=" N GLN D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 6.026A pdb=" N ASP D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN D 79 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 81 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 88 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.688A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 157 removed outlier: 3.721A pdb=" N GLN D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 219 through 222 No H-bonds generated for 'chain 'D' and resid 219 through 222' Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.974A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 259 No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 262 through 265 No H-bonds generated for 'chain 'D' and resid 262 through 265' Processing helix chain 'D' and resid 281 through 292 removed outlier: 3.601A pdb=" N VAL D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.700A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.564A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.513A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.520A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 408 through 424 removed outlier: 3.555A pdb=" N GLU D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 465 removed outlier: 4.036A pdb=" N ASN D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.883A pdb=" N ARG D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 510 through 516' Processing helix chain 'D' and resid 522 through 527 removed outlier: 4.154A pdb=" N SER D 525 " --> pdb=" O MET D 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.583A pdb=" N ILE F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 309 removed outlier: 3.662A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.551A pdb=" N VAL F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS F 327 " --> pdb=" O LEU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 341 through 353 removed outlier: 3.868A pdb=" N ILE F 346 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 347 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER F 348 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS F 349 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER F 352 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.573A pdb=" N GLU F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.847A pdb=" N ILE F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 Processing helix chain 'F' and resid 415 through 429 removed outlier: 3.560A pdb=" N MET F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing helix chain '3' and resid 893 through 905 removed outlier: 3.733A pdb=" N ILE 3 900 " --> pdb=" O ILE 3 896 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 3 902 " --> pdb=" O GLY 3 898 " (cutoff:3.500A) Processing helix chain '3' and resid 916 through 923 Processing helix chain '3' and resid 937 through 947 removed outlier: 3.888A pdb=" N LYS 3 943 " --> pdb=" O LEU 3 939 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE 3 944 " --> pdb=" O ALA 3 940 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 3 945 " --> pdb=" O GLY 3 941 " (cutoff:3.500A) Processing helix chain '7' and resid 744 through 754 Processing helix chain '7' and resid 766 through 768 No H-bonds generated for 'chain '7' and resid 766 through 768' Processing helix chain '7' and resid 776 through 785 removed outlier: 3.733A pdb=" N GLN 7 784 " --> pdb=" O SER 7 780 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '9' and resid 104 through 106 removed outlier: 6.231A pdb=" N GLN 9 284 " --> pdb=" O TYR 9 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '9' and resid 169 through 171 removed outlier: 6.291A pdb=" N VAL 9 221 " --> pdb=" O ILE 9 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '9' and resid 471 through 475 Processing sheet with id= D, first strand: chain 'A' and resid 474 through 477 removed outlier: 7.082A pdb=" N VAL A 595 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL A 477 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 597 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 598 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 647 through 650 Processing sheet with id= F, first strand: chain 'A' and resid 682 through 684 removed outlier: 6.787A pdb=" N GLN A 771 " --> pdb=" O ARG A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 819 through 821 removed outlier: 3.541A pdb=" N GLN A 820 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 476 through 479 removed outlier: 6.957A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 423 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.696A pdb=" N ASN C 103 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 127 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= L, first strand: chain 'E' and resid 185 through 188 removed outlier: 10.045A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 433 through 435 Processing sheet with id= N, first strand: chain 'D' and resid 248 through 251 removed outlier: 6.931A pdb=" N VAL D 98 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR D 251 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU D 100 " --> pdb=" O THR D 251 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.614A pdb=" N THR D 211 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE D 130 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 213 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU D 132 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 215 " --> pdb=" O LEU D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 469 through 471 682 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 11.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7720 1.36 - 1.50: 7370 1.50 - 1.65: 9954 1.65 - 1.79: 97 1.79 - 1.94: 90 Bond restraints: 25231 Sorted by residual: bond pdb=" C LYS 9 509 " pdb=" N PRO 9 510 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" C LEU C 131 " pdb=" N THR C 132 " ideal model delta sigma weight residual 1.331 1.240 0.091 2.83e-02 1.25e+03 1.04e+01 bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 5.05e+00 bond pdb=" C MET 9 225 " pdb=" N ASP 9 226 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.35e-02 5.49e+03 4.72e+00 bond pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.39e-02 5.18e+03 4.66e+00 ... (remaining 25226 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.88: 664 104.88 - 112.25: 12624 112.25 - 119.62: 8999 119.62 - 126.99: 11733 126.99 - 134.36: 422 Bond angle restraints: 34442 Sorted by residual: angle pdb=" C LEU 9 282 " pdb=" N PRO 9 283 " pdb=" CA PRO 9 283 " ideal model delta sigma weight residual 119.84 131.33 -11.49 1.25e+00 6.40e-01 8.45e+01 angle pdb=" N ILE F 411 " pdb=" CA ILE F 411 " pdb=" C ILE F 411 " ideal model delta sigma weight residual 113.16 104.07 9.09 1.49e+00 4.50e-01 3.72e+01 angle pdb=" C ASN 9 232 " pdb=" N THR 9 233 " pdb=" CA THR 9 233 " ideal model delta sigma weight residual 121.31 129.56 -8.25 1.49e+00 4.50e-01 3.07e+01 angle pdb=" C ILE 9 311 " pdb=" N PHE 9 312 " pdb=" CA PHE 9 312 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C ILE D 341 " pdb=" N ILE D 342 " pdb=" CA ILE D 342 " ideal model delta sigma weight residual 120.33 124.63 -4.30 8.00e-01 1.56e+00 2.88e+01 ... (remaining 34437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 13675 25.88 - 51.76: 1286 51.76 - 77.65: 182 77.65 - 103.53: 16 103.53 - 129.41: 2 Dihedral angle restraints: 15161 sinusoidal: 6838 harmonic: 8323 Sorted by residual: dihedral pdb=" CA PHE E 381 " pdb=" C PHE E 381 " pdb=" N ALA E 382 " pdb=" CA ALA E 382 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP 3 955 " pdb=" C ASP 3 955 " pdb=" N ASP 3 956 " pdb=" CA ASP 3 956 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ILE 9 311 " pdb=" C ILE 9 311 " pdb=" N PHE 9 312 " pdb=" CA PHE 9 312 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 15158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3597 0.088 - 0.176: 329 0.176 - 0.264: 27 0.264 - 0.353: 3 0.353 - 0.441: 1 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CB ILE D 508 " pdb=" CA ILE D 508 " pdb=" CG1 ILE D 508 " pdb=" CG2 ILE D 508 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB VAL C 288 " pdb=" CA VAL C 288 " pdb=" CG1 VAL C 288 " pdb=" CG2 VAL C 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB ILE A 578 " pdb=" CA ILE A 578 " pdb=" CG1 ILE A 578 " pdb=" CG2 ILE A 578 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3954 not shown) Planarity restraints: 4024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 372 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 373 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 373 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 373 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 9 509 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO 9 510 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO 9 510 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 9 510 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 480 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO A 481 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.035 5.00e-02 4.00e+02 ... (remaining 4021 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 3 2.23 - 2.89: 9686 2.89 - 3.56: 37062 3.56 - 4.23: 59774 4.23 - 4.90: 92814 Nonbonded interactions: 199339 Sorted by model distance: nonbonded pdb=" CB THR A 538 " pdb=" OP2 DA G 11 " model vdw 1.558 3.470 nonbonded pdb=" O LEU E 444 " pdb=" CD PRO E 446 " model vdw 1.610 3.440 nonbonded pdb=" CB THR A 538 " pdb=" P DA G 11 " model vdw 2.196 3.830 nonbonded pdb=" O1B AGS A2001 " pdb=" O2A AGS A2001 " model vdw 2.250 2.440 nonbonded pdb=" O1A AGS E2001 " pdb=" O2B AGS E2001 " model vdw 2.280 2.440 ... (remaining 199334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 3.220 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 71.180 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 0.091 25231 Z= 0.379 Angle : 0.990 11.492 34442 Z= 0.573 Chirality : 0.054 0.441 3957 Planarity : 0.006 0.080 4024 Dihedral : 18.907 129.412 9717 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Rotamer: Outliers : 0.04 % Allowed : 12.00 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.12), residues: 2738 helix: -3.77 (0.08), residues: 1352 sheet: -2.16 (0.31), residues: 237 loop : -2.29 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 58 HIS 0.011 0.002 HIS C 22 PHE 0.029 0.002 PHE 9 256 TYR 0.026 0.002 TYR 3 938 ARG 0.006 0.001 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 591 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 180 SER cc_start: 0.8700 (m) cc_final: 0.8468 (p) REVERT: 9 204 HIS cc_start: 0.8398 (m170) cc_final: 0.7900 (m170) REVERT: 9 222 LEU cc_start: 0.9678 (tp) cc_final: 0.9441 (tp) REVERT: 9 244 GLU cc_start: 0.8011 (pt0) cc_final: 0.7056 (pt0) REVERT: 9 322 LYS cc_start: 0.8663 (mttp) cc_final: 0.8415 (mttp) REVERT: 9 423 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8328 (tp-100) REVERT: 9 435 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8389 (pt0) REVERT: 9 440 TYR cc_start: 0.9443 (t80) cc_final: 0.9111 (t80) REVERT: 9 498 PHE cc_start: 0.9163 (m-80) cc_final: 0.8888 (m-10) REVERT: A 491 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 564 LEU cc_start: 0.8959 (mp) cc_final: 0.8182 (pp) REVERT: A 571 MET cc_start: 0.8780 (mtm) cc_final: 0.7933 (mtt) REVERT: A 582 PHE cc_start: 0.8857 (m-80) cc_final: 0.8397 (m-80) REVERT: A 585 TRP cc_start: 0.9063 (m-10) cc_final: 0.8532 (m-90) REVERT: A 602 MET cc_start: 0.8086 (tpp) cc_final: 0.7630 (tpp) REVERT: A 623 MET cc_start: 0.8658 (tpt) cc_final: 0.8400 (tpt) REVERT: A 866 TRP cc_start: 0.8445 (t60) cc_final: 0.8034 (t60) REVERT: A 879 LEU cc_start: 0.9464 (mm) cc_final: 0.8995 (mm) REVERT: A 881 LYS cc_start: 0.9513 (tmmt) cc_final: 0.9311 (tmtt) REVERT: A 900 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8049 (mm-30) REVERT: A 902 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8670 (mttt) REVERT: B 315 LEU cc_start: 0.9686 (tp) cc_final: 0.9455 (tt) REVERT: B 377 LYS cc_start: 0.9341 (mtmt) cc_final: 0.8785 (mmtm) REVERT: B 411 TYR cc_start: 0.8411 (m-10) cc_final: 0.7452 (m-10) REVERT: B 440 MET cc_start: 0.8761 (tmm) cc_final: 0.8433 (tmm) REVERT: B 441 LEU cc_start: 0.9425 (mm) cc_final: 0.8565 (mt) REVERT: B 460 TYR cc_start: 0.9269 (m-10) cc_final: 0.9031 (m-10) REVERT: B 466 ASP cc_start: 0.8674 (p0) cc_final: 0.8209 (p0) REVERT: B 496 MET cc_start: 0.7428 (ppp) cc_final: 0.6824 (tmm) REVERT: B 524 MET cc_start: 0.8345 (ptm) cc_final: 0.7488 (ptt) REVERT: B 547 ARG cc_start: 0.3938 (tmt-80) cc_final: 0.3298 (ptm160) REVERT: B 561 HIS cc_start: 0.9177 (m170) cc_final: 0.8628 (t-90) REVERT: B 578 MET cc_start: 0.8307 (ptp) cc_final: 0.7501 (ptm) REVERT: B 581 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 604 TYR cc_start: 0.8294 (m-10) cc_final: 0.7944 (m-10) REVERT: C 111 ASP cc_start: 0.8445 (p0) cc_final: 0.8061 (p0) REVERT: C 201 MET cc_start: 0.8828 (ptt) cc_final: 0.8525 (ptt) REVERT: C 206 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8138 (mtmm) REVERT: C 207 ASP cc_start: 0.8013 (t0) cc_final: 0.7589 (t0) REVERT: C 214 ASN cc_start: 0.8734 (p0) cc_final: 0.8148 (t0) REVERT: C 292 LEU cc_start: 0.9172 (tp) cc_final: 0.8909 (tp) REVERT: C 296 ASP cc_start: 0.9362 (p0) cc_final: 0.8767 (p0) REVERT: C 297 ARG cc_start: 0.8896 (mtp180) cc_final: 0.8503 (mtm-85) REVERT: C 321 LEU cc_start: 0.9364 (mm) cc_final: 0.9143 (mm) REVERT: C 371 HIS cc_start: 0.8675 (m-70) cc_final: 0.8408 (m90) REVERT: C 540 PHE cc_start: 0.8753 (t80) cc_final: 0.8365 (t80) REVERT: E 110 LYS cc_start: 0.9302 (tmtt) cc_final: 0.8736 (tppt) REVERT: E 170 MET cc_start: 0.8747 (ptp) cc_final: 0.8531 (ptp) REVERT: E 195 ASP cc_start: 0.9184 (p0) cc_final: 0.8821 (p0) REVERT: E 323 ASP cc_start: 0.7414 (t0) cc_final: 0.7153 (t0) REVERT: E 336 TYR cc_start: 0.8904 (t80) cc_final: 0.8269 (t80) REVERT: E 422 GLN cc_start: 0.9141 (tp40) cc_final: 0.8243 (tp-100) REVERT: D 105 GLN cc_start: 0.9344 (mm110) cc_final: 0.9086 (mm-40) REVERT: D 123 TYR cc_start: 0.9180 (m-80) cc_final: 0.8569 (m-80) REVERT: D 218 GLU cc_start: 0.8866 (mp0) cc_final: 0.8242 (mp0) REVERT: D 233 ASN cc_start: 0.8598 (m110) cc_final: 0.8397 (t0) REVERT: D 253 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8000 (mtmt) REVERT: D 259 TYR cc_start: 0.9144 (m-10) cc_final: 0.8702 (m-10) REVERT: D 262 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8087 (tptp) REVERT: D 268 PHE cc_start: 0.8951 (t80) cc_final: 0.8684 (t80) REVERT: D 270 GLN cc_start: 0.9020 (mm110) cc_final: 0.8698 (tm-30) REVERT: D 313 LEU cc_start: 0.9260 (tp) cc_final: 0.9011 (tp) REVERT: D 365 ASP cc_start: 0.8301 (m-30) cc_final: 0.8053 (m-30) REVERT: D 390 ILE cc_start: 0.9423 (mt) cc_final: 0.9172 (tp) REVERT: D 425 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8170 (tpm170) REVERT: D 467 ASP cc_start: 0.8574 (m-30) cc_final: 0.8358 (m-30) REVERT: D 469 PHE cc_start: 0.8513 (m-80) cc_final: 0.8253 (m-80) REVERT: D 475 VAL cc_start: 0.8708 (t) cc_final: 0.7681 (m) REVERT: D 496 MET cc_start: 0.7828 (mmt) cc_final: 0.7498 (mmm) REVERT: D 506 MET cc_start: 0.7749 (tpp) cc_final: 0.7310 (tpp) REVERT: D 512 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 337 ARG cc_start: 0.6212 (mmt90) cc_final: 0.5373 (ttp-170) REVERT: F 364 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8427 (mp0) REVERT: F 398 ILE cc_start: 0.9442 (pt) cc_final: 0.9232 (pt) REVERT: 3 909 PHE cc_start: 0.7542 (m-80) cc_final: 0.7074 (m-80) REVERT: 3 921 GLU cc_start: 0.9059 (pt0) cc_final: 0.8188 (pt0) REVERT: 3 922 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8265 (mmt90) REVERT: 3 952 MET cc_start: 0.8081 (mmt) cc_final: 0.7745 (mtp) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.4085 time to fit residues: 358.6873 Evaluate side-chains 406 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 165 optimal weight: 0.1980 chunk 257 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 232 ASN 9 295 GLN 9 388 ASN 9 401 ASN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN A 581 ASN A 584 ASN A 725 HIS ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 282 ASN B 297 GLN B 398 ASN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 493 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 78 ASN ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN C 454 HIS ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 114 ASN ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN E 417 ASN E 422 GLN ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 158 HIS ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 GLN F 309 ASN F 407 GLN 3 924 ASN 3 949 ASN 3 950 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25231 Z= 0.247 Angle : 0.664 9.109 34442 Z= 0.359 Chirality : 0.042 0.199 3957 Planarity : 0.005 0.083 4024 Dihedral : 17.701 136.029 4026 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.12 % Allowed : 7.17 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -3.34 (0.14), residues: 2738 helix: -2.24 (0.11), residues: 1453 sheet: -1.72 (0.33), residues: 216 loop : -2.03 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 529 HIS 0.009 0.001 HIS C 69 PHE 0.021 0.001 PHE D 72 TYR 0.026 0.002 TYR D 232 ARG 0.006 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 525 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 201 ASN cc_start: 0.8523 (t0) cc_final: 0.7848 (t0) REVERT: 9 204 HIS cc_start: 0.8411 (m170) cc_final: 0.7865 (m90) REVERT: 9 222 LEU cc_start: 0.9632 (tp) cc_final: 0.9397 (tp) REVERT: 9 244 GLU cc_start: 0.8098 (pt0) cc_final: 0.7398 (pt0) REVERT: 9 261 MET cc_start: 0.7714 (mpp) cc_final: 0.6702 (mpp) REVERT: 9 296 MET cc_start: 0.6841 (mtt) cc_final: 0.6494 (mtt) REVERT: 9 423 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8333 (tp-100) REVERT: 9 435 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8448 (pt0) REVERT: 9 496 ARG cc_start: 0.8892 (tpt90) cc_final: 0.8673 (ttp80) REVERT: 9 498 PHE cc_start: 0.9017 (m-80) cc_final: 0.8706 (m-10) REVERT: 9 499 TYR cc_start: 0.9180 (m-10) cc_final: 0.8459 (m-80) REVERT: 9 502 MET cc_start: 0.9065 (ppp) cc_final: 0.8757 (mmt) REVERT: A 411 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7803 (mttp) REVERT: A 513 ILE cc_start: 0.8725 (mm) cc_final: 0.8228 (tt) REVERT: A 518 MET cc_start: 0.8431 (mmp) cc_final: 0.8174 (mmp) REVERT: A 526 GLU cc_start: 0.8905 (pt0) cc_final: 0.7985 (tp30) REVERT: A 571 MET cc_start: 0.8653 (mtm) cc_final: 0.8157 (mtt) REVERT: A 578 ILE cc_start: 0.8871 (tt) cc_final: 0.8536 (tt) REVERT: A 582 PHE cc_start: 0.8561 (m-80) cc_final: 0.8264 (m-80) REVERT: A 585 TRP cc_start: 0.8990 (m-10) cc_final: 0.8404 (m-90) REVERT: A 602 MET cc_start: 0.8168 (tpp) cc_final: 0.7807 (tpp) REVERT: A 696 VAL cc_start: 0.9654 (t) cc_final: 0.9431 (p) REVERT: A 879 LEU cc_start: 0.9297 (mm) cc_final: 0.8930 (mm) REVERT: A 893 LYS cc_start: 0.9282 (tttt) cc_final: 0.9055 (ttmm) REVERT: A 902 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8564 (mttt) REVERT: B 273 GLU cc_start: 0.8908 (tt0) cc_final: 0.8683 (tt0) REVERT: B 377 LYS cc_start: 0.9442 (mtmt) cc_final: 0.8743 (mmtm) REVERT: B 417 ASP cc_start: 0.7433 (t0) cc_final: 0.4992 (p0) REVERT: B 438 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8698 (tp40) REVERT: B 440 MET cc_start: 0.8778 (tmm) cc_final: 0.8258 (tmm) REVERT: B 460 TYR cc_start: 0.9164 (m-10) cc_final: 0.8743 (m-10) REVERT: B 496 MET cc_start: 0.7296 (ppp) cc_final: 0.6147 (tmm) REVERT: B 524 MET cc_start: 0.8320 (ptm) cc_final: 0.7625 (ptt) REVERT: B 547 ARG cc_start: 0.3847 (tmt-80) cc_final: 0.3317 (ptm160) REVERT: B 561 HIS cc_start: 0.9159 (m170) cc_final: 0.8601 (t-170) REVERT: B 578 MET cc_start: 0.8126 (ptp) cc_final: 0.7723 (ptm) REVERT: C 83 LEU cc_start: 0.8871 (pp) cc_final: 0.8647 (pp) REVERT: C 113 THR cc_start: 0.7625 (p) cc_final: 0.7373 (p) REVERT: C 204 ASN cc_start: 0.8646 (t0) cc_final: 0.8025 (t0) REVERT: C 206 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8106 (mtmm) REVERT: C 213 PHE cc_start: 0.8965 (m-80) cc_final: 0.8463 (m-80) REVERT: C 214 ASN cc_start: 0.8757 (p0) cc_final: 0.8428 (t0) REVERT: C 296 ASP cc_start: 0.9432 (p0) cc_final: 0.9124 (p0) REVERT: C 297 ARG cc_start: 0.8972 (mtp180) cc_final: 0.8710 (mtm180) REVERT: C 320 MET cc_start: 0.8645 (ptp) cc_final: 0.8132 (ptp) REVERT: C 321 LEU cc_start: 0.9612 (mm) cc_final: 0.9385 (mm) REVERT: C 361 MET cc_start: 0.9023 (ptp) cc_final: 0.8539 (ptp) REVERT: C 371 HIS cc_start: 0.8642 (m-70) cc_final: 0.8420 (m90) REVERT: C 540 PHE cc_start: 0.8707 (t80) cc_final: 0.8336 (t80) REVERT: E 110 LYS cc_start: 0.9244 (tmtt) cc_final: 0.8811 (tppt) REVERT: E 195 ASP cc_start: 0.9084 (p0) cc_final: 0.8826 (p0) REVERT: E 323 ASP cc_start: 0.7195 (t0) cc_final: 0.6962 (t0) REVERT: E 422 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8380 (tp40) REVERT: E 473 TYR cc_start: 0.8801 (m-80) cc_final: 0.8241 (m-80) REVERT: D 123 TYR cc_start: 0.9092 (m-80) cc_final: 0.8422 (m-80) REVERT: D 218 GLU cc_start: 0.8882 (mp0) cc_final: 0.8485 (mp0) REVERT: D 233 ASN cc_start: 0.8643 (m110) cc_final: 0.8403 (t0) REVERT: D 253 LYS cc_start: 0.8866 (mmtt) cc_final: 0.7973 (mtmt) REVERT: D 259 TYR cc_start: 0.9093 (m-10) cc_final: 0.8465 (m-10) REVERT: D 262 LYS cc_start: 0.8711 (tmtt) cc_final: 0.7960 (tptp) REVERT: D 268 PHE cc_start: 0.8896 (t80) cc_final: 0.8442 (t80) REVERT: D 270 GLN cc_start: 0.9174 (mm110) cc_final: 0.8921 (tm-30) REVERT: D 313 LEU cc_start: 0.9150 (tp) cc_final: 0.8914 (tp) REVERT: D 326 MET cc_start: 0.8951 (mtp) cc_final: 0.8504 (ttt) REVERT: D 365 ASP cc_start: 0.8261 (m-30) cc_final: 0.7951 (m-30) REVERT: D 425 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.8124 (tpt90) REVERT: D 467 ASP cc_start: 0.8547 (m-30) cc_final: 0.8092 (m-30) REVERT: D 506 MET cc_start: 0.7637 (tpp) cc_final: 0.7219 (tpp) REVERT: D 512 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7637 (mm-30) REVERT: F 304 ASP cc_start: 0.9348 (t0) cc_final: 0.9131 (m-30) REVERT: F 335 ARG cc_start: 0.9125 (mtt-85) cc_final: 0.8687 (mmm160) REVERT: F 350 MET cc_start: 0.9325 (tmm) cc_final: 0.8963 (tmm) REVERT: F 354 MET cc_start: 0.8582 (mmp) cc_final: 0.8021 (mmp) REVERT: F 356 THR cc_start: 0.6009 (p) cc_final: 0.5790 (p) REVERT: F 364 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8719 (mp0) outliers start: 3 outliers final: 1 residues processed: 526 average time/residue: 0.4059 time to fit residues: 331.3643 Evaluate side-chains 382 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 175 optimal weight: 0.0060 chunk 71 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 256 optimal weight: 0.0980 chunk 88 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 203 GLN 9 295 GLN 9 401 ASN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 815 ASN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN B 532 GLN C 63 GLN C 69 HIS C 253 GLN C 312 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25231 Z= 0.160 Angle : 0.610 8.470 34442 Z= 0.320 Chirality : 0.041 0.179 3957 Planarity : 0.004 0.066 4024 Dihedral : 17.403 134.170 4026 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -2.62 (0.15), residues: 2738 helix: -1.65 (0.12), residues: 1422 sheet: -1.45 (0.35), residues: 215 loop : -1.70 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 305 HIS 0.005 0.001 HIS A 777 PHE 0.024 0.001 PHE 9 485 TYR 0.023 0.001 TYR B 304 ARG 0.007 0.000 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 540 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 201 ASN cc_start: 0.8413 (t0) cc_final: 0.7766 (t0) REVERT: 9 204 HIS cc_start: 0.8236 (m170) cc_final: 0.7623 (m90) REVERT: 9 222 LEU cc_start: 0.9611 (tp) cc_final: 0.9344 (tp) REVERT: 9 261 MET cc_start: 0.7671 (mpp) cc_final: 0.7063 (mpp) REVERT: 9 322 LYS cc_start: 0.8435 (mttp) cc_final: 0.8146 (mttp) REVERT: 9 419 CYS cc_start: 0.9405 (t) cc_final: 0.8528 (t) REVERT: 9 423 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8231 (tp-100) REVERT: 9 435 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8333 (pt0) REVERT: 9 488 LYS cc_start: 0.7001 (tptp) cc_final: 0.6711 (tptp) REVERT: 9 498 PHE cc_start: 0.8980 (m-80) cc_final: 0.8604 (m-10) REVERT: 9 499 TYR cc_start: 0.9077 (m-10) cc_final: 0.8390 (m-80) REVERT: A 411 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7837 (mttp) REVERT: A 490 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7799 (mtp85) REVERT: A 513 ILE cc_start: 0.8667 (mm) cc_final: 0.8162 (tt) REVERT: A 526 GLU cc_start: 0.8703 (pt0) cc_final: 0.8097 (tm-30) REVERT: A 543 MET cc_start: 0.9272 (ptm) cc_final: 0.8982 (ptm) REVERT: A 571 MET cc_start: 0.8667 (mtm) cc_final: 0.7765 (mtt) REVERT: A 578 ILE cc_start: 0.8861 (tt) cc_final: 0.8392 (tt) REVERT: A 582 PHE cc_start: 0.8542 (m-80) cc_final: 0.8312 (m-80) REVERT: A 585 TRP cc_start: 0.8928 (m-10) cc_final: 0.8427 (m-90) REVERT: A 696 VAL cc_start: 0.9565 (t) cc_final: 0.9342 (p) REVERT: A 843 MET cc_start: 0.8731 (mpp) cc_final: 0.8419 (mpp) REVERT: A 879 LEU cc_start: 0.9285 (mm) cc_final: 0.8917 (mm) REVERT: A 881 LYS cc_start: 0.9490 (tmmt) cc_final: 0.9089 (tmtt) REVERT: A 882 GLN cc_start: 0.6585 (mt0) cc_final: 0.6203 (mm-40) REVERT: A 902 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8567 (mttt) REVERT: B 300 MET cc_start: 0.9182 (ttp) cc_final: 0.8896 (ttm) REVERT: B 323 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7989 (tmm-80) REVERT: B 377 LYS cc_start: 0.9428 (mtmt) cc_final: 0.9208 (mtmt) REVERT: B 417 ASP cc_start: 0.7528 (t0) cc_final: 0.5561 (p0) REVERT: B 440 MET cc_start: 0.8724 (tmm) cc_final: 0.8404 (tmm) REVERT: B 458 HIS cc_start: 0.8080 (t-90) cc_final: 0.7778 (t-90) REVERT: B 460 TYR cc_start: 0.9163 (m-10) cc_final: 0.8956 (m-10) REVERT: B 496 MET cc_start: 0.7117 (ppp) cc_final: 0.5708 (tmm) REVERT: B 524 MET cc_start: 0.8282 (ptm) cc_final: 0.7540 (ptt) REVERT: B 547 ARG cc_start: 0.3804 (tmt-80) cc_final: 0.3368 (ptm160) REVERT: B 561 HIS cc_start: 0.9172 (m170) cc_final: 0.8590 (t-170) REVERT: B 604 TYR cc_start: 0.8023 (m-10) cc_final: 0.7447 (m-10) REVERT: C 91 LEU cc_start: 0.9557 (tp) cc_final: 0.9349 (tp) REVERT: C 106 PHE cc_start: 0.8401 (m-80) cc_final: 0.8178 (m-80) REVERT: C 206 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8231 (mttp) REVERT: C 213 PHE cc_start: 0.8865 (m-80) cc_final: 0.8491 (m-80) REVERT: C 214 ASN cc_start: 0.8690 (p0) cc_final: 0.8279 (t0) REVERT: C 296 ASP cc_start: 0.9388 (p0) cc_final: 0.9180 (p0) REVERT: C 321 LEU cc_start: 0.9575 (mm) cc_final: 0.9218 (mm) REVERT: C 361 MET cc_start: 0.9027 (ptp) cc_final: 0.8552 (ptp) REVERT: C 498 LEU cc_start: 0.9003 (mm) cc_final: 0.8758 (mm) REVERT: C 523 GLN cc_start: 0.8213 (pt0) cc_final: 0.7805 (pt0) REVERT: C 540 PHE cc_start: 0.8684 (t80) cc_final: 0.8309 (t80) REVERT: E 183 CYS cc_start: 0.8785 (m) cc_final: 0.8213 (t) REVERT: E 195 ASP cc_start: 0.9103 (p0) cc_final: 0.8833 (p0) REVERT: E 210 MET cc_start: 0.9403 (mtm) cc_final: 0.9200 (mmp) REVERT: E 473 TYR cc_start: 0.8720 (m-80) cc_final: 0.8290 (m-80) REVERT: D 85 ILE cc_start: 0.9492 (mt) cc_final: 0.9231 (mm) REVERT: D 123 TYR cc_start: 0.8921 (m-80) cc_final: 0.8410 (m-80) REVERT: D 237 MET cc_start: 0.8345 (tpp) cc_final: 0.8118 (tpp) REVERT: D 240 HIS cc_start: 0.8914 (m90) cc_final: 0.8632 (m-70) REVERT: D 253 LYS cc_start: 0.8878 (mmtt) cc_final: 0.7942 (mtmt) REVERT: D 259 TYR cc_start: 0.9122 (m-10) cc_final: 0.8489 (m-10) REVERT: D 262 LYS cc_start: 0.8520 (tmtt) cc_final: 0.7892 (tptp) REVERT: D 268 PHE cc_start: 0.8911 (t80) cc_final: 0.8476 (t80) REVERT: D 270 GLN cc_start: 0.9161 (mm110) cc_final: 0.8961 (tm-30) REVERT: D 365 ASP cc_start: 0.8220 (m-30) cc_final: 0.7908 (m-30) REVERT: D 390 ILE cc_start: 0.9466 (mt) cc_final: 0.9222 (tp) REVERT: D 425 ARG cc_start: 0.8466 (ptm-80) cc_final: 0.8128 (tpt90) REVERT: D 467 ASP cc_start: 0.8156 (m-30) cc_final: 0.7779 (m-30) REVERT: D 512 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7739 (mm-30) REVERT: F 304 ASP cc_start: 0.9311 (t0) cc_final: 0.9107 (m-30) REVERT: F 332 PHE cc_start: 0.9248 (m-80) cc_final: 0.8992 (m-10) REVERT: F 335 ARG cc_start: 0.9117 (mtt-85) cc_final: 0.8662 (mmm160) REVERT: F 336 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8673 (mtm110) REVERT: F 350 MET cc_start: 0.9366 (tmm) cc_final: 0.9049 (tmm) REVERT: F 354 MET cc_start: 0.8449 (mmp) cc_final: 0.8049 (mmp) REVERT: F 356 THR cc_start: 0.6266 (p) cc_final: 0.6049 (p) REVERT: F 364 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8645 (mp0) REVERT: F 410 ASN cc_start: 0.8597 (t0) cc_final: 0.8011 (t0) REVERT: 3 909 PHE cc_start: 0.7659 (m-80) cc_final: 0.7094 (m-80) outliers start: 3 outliers final: 2 residues processed: 540 average time/residue: 0.3723 time to fit residues: 309.2039 Evaluate side-chains 396 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 394 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 123 optimal weight: 0.0870 chunk 173 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 274 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 203 GLN 9 295 GLN 9 413 GLN A 815 ASN A 852 GLN B 403 GLN B 405 GLN B 426 ASN B 438 GLN C 63 GLN C 231 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25231 Z= 0.217 Angle : 0.608 10.534 34442 Z= 0.324 Chirality : 0.042 0.206 3957 Planarity : 0.004 0.063 4024 Dihedral : 17.284 135.262 4026 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2738 helix: -1.20 (0.13), residues: 1446 sheet: -1.36 (0.35), residues: 218 loop : -1.69 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 529 HIS 0.008 0.001 HIS C 371 PHE 0.029 0.001 PHE F 389 TYR 0.014 0.001 TYR 3 938 ARG 0.008 0.000 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8698 (mmp) cc_final: 0.8492 (mmm) REVERT: 9 201 ASN cc_start: 0.8480 (t0) cc_final: 0.8203 (t0) REVERT: 9 222 LEU cc_start: 0.9636 (tp) cc_final: 0.9384 (tp) REVERT: 9 244 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8104 (pt0) REVERT: 9 261 MET cc_start: 0.7987 (mpp) cc_final: 0.7344 (mpp) REVERT: 9 322 LYS cc_start: 0.8458 (mttp) cc_final: 0.8130 (mttp) REVERT: 9 419 CYS cc_start: 0.9425 (t) cc_final: 0.8583 (t) REVERT: 9 423 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8348 (tp-100) REVERT: 9 432 THR cc_start: 0.9342 (p) cc_final: 0.8753 (p) REVERT: 9 435 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8456 (pt0) REVERT: 9 488 LYS cc_start: 0.7040 (tptp) cc_final: 0.6690 (tptm) REVERT: 9 499 TYR cc_start: 0.8927 (m-10) cc_final: 0.8324 (m-80) REVERT: 9 511 PHE cc_start: 0.7780 (t80) cc_final: 0.7484 (t80) REVERT: A 411 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7813 (mttp) REVERT: A 513 ILE cc_start: 0.8685 (mm) cc_final: 0.8179 (tt) REVERT: A 526 GLU cc_start: 0.8793 (pt0) cc_final: 0.8236 (tm-30) REVERT: A 571 MET cc_start: 0.8643 (mtm) cc_final: 0.7940 (mtt) REVERT: A 696 VAL cc_start: 0.9581 (t) cc_final: 0.9367 (p) REVERT: A 879 LEU cc_start: 0.9310 (mm) cc_final: 0.8959 (mm) REVERT: A 881 LYS cc_start: 0.9500 (tmmt) cc_final: 0.9112 (tmtt) REVERT: A 882 GLN cc_start: 0.6691 (mt0) cc_final: 0.6301 (mm-40) REVERT: A 902 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8559 (mttt) REVERT: B 269 VAL cc_start: 0.8284 (t) cc_final: 0.7455 (t) REVERT: B 300 MET cc_start: 0.9072 (ttp) cc_final: 0.8861 (ttm) REVERT: B 334 LEU cc_start: 0.9465 (tp) cc_final: 0.9254 (tt) REVERT: B 377 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9143 (mtmt) REVERT: B 417 ASP cc_start: 0.7363 (t0) cc_final: 0.5160 (p0) REVERT: B 440 MET cc_start: 0.8713 (tmm) cc_final: 0.8375 (tmm) REVERT: B 458 HIS cc_start: 0.8073 (t-90) cc_final: 0.7427 (t70) REVERT: B 460 TYR cc_start: 0.9154 (m-10) cc_final: 0.8714 (m-10) REVERT: B 496 MET cc_start: 0.6872 (ppp) cc_final: 0.5573 (tmm) REVERT: B 547 ARG cc_start: 0.4284 (tmt-80) cc_final: 0.3750 (ptm160) REVERT: B 561 HIS cc_start: 0.9184 (m170) cc_final: 0.8543 (t-170) REVERT: B 563 CYS cc_start: 0.9223 (m) cc_final: 0.8871 (m) REVERT: B 578 MET cc_start: 0.7351 (ptm) cc_final: 0.7083 (ptm) REVERT: B 604 TYR cc_start: 0.7839 (m-10) cc_final: 0.7198 (m-10) REVERT: C 204 ASN cc_start: 0.8479 (t0) cc_final: 0.8266 (t0) REVERT: C 206 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8325 (mttp) REVERT: C 213 PHE cc_start: 0.8995 (m-80) cc_final: 0.8621 (m-80) REVERT: C 214 ASN cc_start: 0.8700 (p0) cc_final: 0.8308 (t0) REVERT: C 361 MET cc_start: 0.9051 (ptp) cc_final: 0.8615 (ptp) REVERT: C 428 TYR cc_start: 0.8495 (t80) cc_final: 0.8210 (t80) REVERT: C 498 LEU cc_start: 0.9347 (mm) cc_final: 0.9075 (mm) REVERT: C 523 GLN cc_start: 0.8262 (pt0) cc_final: 0.7882 (pt0) REVERT: C 540 PHE cc_start: 0.8675 (t80) cc_final: 0.8306 (t80) REVERT: E 195 ASP cc_start: 0.9081 (p0) cc_final: 0.8759 (p0) REVERT: E 473 TYR cc_start: 0.8749 (m-80) cc_final: 0.8247 (m-80) REVERT: D 123 TYR cc_start: 0.8976 (m-80) cc_final: 0.8515 (m-80) REVERT: D 248 PHE cc_start: 0.9029 (m-80) cc_final: 0.8673 (m-80) REVERT: D 250 CYS cc_start: 0.8523 (m) cc_final: 0.8221 (m) REVERT: D 253 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8135 (mtmt) REVERT: D 259 TYR cc_start: 0.9119 (m-10) cc_final: 0.8787 (m-10) REVERT: D 268 PHE cc_start: 0.8985 (t80) cc_final: 0.8522 (t80) REVERT: D 270 GLN cc_start: 0.9129 (mm110) cc_final: 0.8848 (tm-30) REVERT: D 365 ASP cc_start: 0.8196 (m-30) cc_final: 0.7922 (m-30) REVERT: D 390 ILE cc_start: 0.9470 (mt) cc_final: 0.9258 (tp) REVERT: D 467 ASP cc_start: 0.8220 (m-30) cc_final: 0.7763 (m-30) REVERT: D 508 ILE cc_start: 0.9668 (tt) cc_final: 0.9462 (tt) REVERT: F 304 ASP cc_start: 0.9308 (t0) cc_final: 0.9108 (m-30) REVERT: F 335 ARG cc_start: 0.9125 (mtt-85) cc_final: 0.8649 (mmm160) REVERT: F 336 ARG cc_start: 0.8953 (mtp-110) cc_final: 0.7999 (mtm110) REVERT: F 350 MET cc_start: 0.9413 (tmm) cc_final: 0.9131 (tmm) REVERT: F 354 MET cc_start: 0.8494 (mmp) cc_final: 0.8022 (mmp) REVERT: F 356 THR cc_start: 0.6314 (p) cc_final: 0.6077 (p) REVERT: F 364 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8624 (mp0) REVERT: F 410 ASN cc_start: 0.8298 (t0) cc_final: 0.7554 (t0) REVERT: 3 905 GLN cc_start: 0.7669 (mt0) cc_final: 0.7417 (mt0) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3703 time to fit residues: 285.1564 Evaluate side-chains 377 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 203 GLN ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 303 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 63 GLN ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN D 80 GLN D 233 ASN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25231 Z= 0.162 Angle : 0.596 9.614 34442 Z= 0.312 Chirality : 0.042 0.216 3957 Planarity : 0.004 0.063 4024 Dihedral : 17.147 134.137 4026 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2738 helix: -0.93 (0.13), residues: 1437 sheet: -1.18 (0.35), residues: 222 loop : -1.49 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 460 HIS 0.009 0.001 HIS A 777 PHE 0.023 0.001 PHE D 72 TYR 0.021 0.001 TYR 9 291 ARG 0.009 0.000 ARG 9 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 222 LEU cc_start: 0.9609 (tp) cc_final: 0.9345 (tp) REVERT: 9 261 MET cc_start: 0.8008 (mpp) cc_final: 0.7509 (mpp) REVERT: 9 315 MET cc_start: 0.8664 (tmm) cc_final: 0.8449 (tmm) REVERT: 9 419 CYS cc_start: 0.9411 (t) cc_final: 0.8586 (t) REVERT: 9 423 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8324 (tp-100) REVERT: 9 435 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8443 (pt0) REVERT: 9 495 MET cc_start: 0.6804 (pmm) cc_final: 0.6549 (pmm) REVERT: 9 499 TYR cc_start: 0.8901 (m-10) cc_final: 0.8236 (m-80) REVERT: A 411 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7811 (mttp) REVERT: A 513 ILE cc_start: 0.8674 (mm) cc_final: 0.8145 (tt) REVERT: A 526 GLU cc_start: 0.8594 (pt0) cc_final: 0.7984 (mm-30) REVERT: A 571 MET cc_start: 0.8684 (mtm) cc_final: 0.8203 (mtt) REVERT: A 578 ILE cc_start: 0.9159 (mm) cc_final: 0.8838 (tt) REVERT: A 623 MET cc_start: 0.9080 (tpp) cc_final: 0.8706 (tpt) REVERT: A 696 VAL cc_start: 0.9485 (t) cc_final: 0.9260 (p) REVERT: A 808 LEU cc_start: 0.9524 (tt) cc_final: 0.9038 (pp) REVERT: A 843 MET cc_start: 0.8728 (mpp) cc_final: 0.8210 (mpp) REVERT: A 879 LEU cc_start: 0.9310 (mm) cc_final: 0.8925 (mm) REVERT: A 881 LYS cc_start: 0.9460 (tmmt) cc_final: 0.9083 (tmtt) REVERT: A 893 LYS cc_start: 0.9287 (tttt) cc_final: 0.9028 (ttmm) REVERT: A 902 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8541 (mttt) REVERT: B 334 LEU cc_start: 0.9451 (tp) cc_final: 0.9226 (tt) REVERT: B 417 ASP cc_start: 0.7392 (t0) cc_final: 0.5412 (p0) REVERT: B 440 MET cc_start: 0.8639 (tmm) cc_final: 0.8381 (tmm) REVERT: B 460 TYR cc_start: 0.9117 (m-10) cc_final: 0.8732 (m-10) REVERT: B 496 MET cc_start: 0.7219 (ppp) cc_final: 0.5700 (tmm) REVERT: B 547 ARG cc_start: 0.3802 (tmt-80) cc_final: 0.3310 (ptm160) REVERT: B 604 TYR cc_start: 0.7769 (m-10) cc_final: 0.7226 (m-10) REVERT: C 206 LYS cc_start: 0.9086 (mmtp) cc_final: 0.8687 (mttp) REVERT: C 213 PHE cc_start: 0.8919 (m-80) cc_final: 0.8633 (m-80) REVERT: C 214 ASN cc_start: 0.8590 (p0) cc_final: 0.8287 (t0) REVERT: C 320 MET cc_start: 0.8588 (ttt) cc_final: 0.8353 (tpp) REVERT: C 361 MET cc_start: 0.9021 (ptp) cc_final: 0.8583 (ptp) REVERT: C 428 TYR cc_start: 0.8511 (t80) cc_final: 0.8195 (t80) REVERT: C 498 LEU cc_start: 0.9268 (mm) cc_final: 0.8999 (mm) REVERT: C 523 GLN cc_start: 0.8234 (pt0) cc_final: 0.7834 (pt0) REVERT: C 540 PHE cc_start: 0.8658 (t80) cc_final: 0.8276 (t80) REVERT: C 585 MET cc_start: 0.6881 (ttt) cc_final: 0.5745 (tmm) REVERT: E 183 CYS cc_start: 0.8812 (m) cc_final: 0.8538 (t) REVERT: E 195 ASP cc_start: 0.9118 (p0) cc_final: 0.8792 (p0) REVERT: E 324 LEU cc_start: 0.7981 (pt) cc_final: 0.7554 (pt) REVERT: E 473 TYR cc_start: 0.8708 (m-80) cc_final: 0.8241 (m-80) REVERT: D 123 TYR cc_start: 0.8930 (m-80) cc_final: 0.8553 (m-80) REVERT: D 248 PHE cc_start: 0.9104 (m-80) cc_final: 0.8852 (m-80) REVERT: D 253 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8125 (mtmt) REVERT: D 259 TYR cc_start: 0.9119 (m-10) cc_final: 0.8751 (m-10) REVERT: D 268 PHE cc_start: 0.8981 (t80) cc_final: 0.8506 (t80) REVERT: D 270 GLN cc_start: 0.9151 (mm110) cc_final: 0.8862 (tm-30) REVERT: D 365 ASP cc_start: 0.8116 (m-30) cc_final: 0.7854 (m-30) REVERT: D 425 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7815 (tpt90) REVERT: D 467 ASP cc_start: 0.8044 (m-30) cc_final: 0.7698 (m-30) REVERT: D 508 ILE cc_start: 0.9711 (tt) cc_final: 0.9471 (tt) REVERT: D 512 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7812 (mm-30) REVERT: F 304 ASP cc_start: 0.9299 (t0) cc_final: 0.9097 (m-30) REVERT: F 335 ARG cc_start: 0.9117 (mtt-85) cc_final: 0.8653 (mmm160) REVERT: F 350 MET cc_start: 0.9405 (tmm) cc_final: 0.9163 (tmm) REVERT: F 354 MET cc_start: 0.8444 (mmp) cc_final: 0.8085 (mmp) REVERT: F 356 THR cc_start: 0.6186 (p) cc_final: 0.5961 (p) REVERT: F 364 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8625 (mp0) REVERT: F 410 ASN cc_start: 0.8524 (t0) cc_final: 0.8287 (t0) REVERT: 3 905 GLN cc_start: 0.7624 (mt0) cc_final: 0.7080 (mt0) REVERT: 3 920 PHE cc_start: 0.8320 (m-80) cc_final: 0.7866 (m-80) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3635 time to fit residues: 282.3974 Evaluate side-chains 367 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.2980 chunk 247 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 67 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 228 optimal weight: 0.0980 chunk 127 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 63 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 905 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25231 Z= 0.153 Angle : 0.588 9.126 34442 Z= 0.302 Chirality : 0.041 0.209 3957 Planarity : 0.004 0.062 4024 Dihedral : 16.998 132.752 4026 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2738 helix: -0.79 (0.13), residues: 1434 sheet: -1.06 (0.36), residues: 217 loop : -1.49 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 378 HIS 0.007 0.001 HIS A 777 PHE 0.040 0.001 PHE B 475 TYR 0.026 0.001 TYR B 473 ARG 0.007 0.000 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 184 LYS cc_start: 0.9375 (mptt) cc_final: 0.9149 (mmtt) REVERT: 9 222 LEU cc_start: 0.9593 (tp) cc_final: 0.9333 (tp) REVERT: 9 224 GLU cc_start: 0.7272 (tp30) cc_final: 0.7026 (tp30) REVERT: 9 244 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7974 (pt0) REVERT: 9 261 MET cc_start: 0.7978 (mpp) cc_final: 0.7601 (mpp) REVERT: 9 315 MET cc_start: 0.8702 (tmm) cc_final: 0.8475 (tmm) REVERT: 9 322 LYS cc_start: 0.8543 (mttp) cc_final: 0.7785 (pttt) REVERT: 9 323 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8197 (mmmt) REVERT: 9 419 CYS cc_start: 0.9389 (t) cc_final: 0.8570 (t) REVERT: 9 423 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8327 (tp-100) REVERT: 9 432 THR cc_start: 0.9336 (p) cc_final: 0.8741 (p) REVERT: 9 435 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8431 (pt0) REVERT: 9 499 TYR cc_start: 0.8880 (m-10) cc_final: 0.8272 (m-80) REVERT: 9 511 PHE cc_start: 0.7777 (t80) cc_final: 0.7513 (t80) REVERT: A 513 ILE cc_start: 0.8639 (mm) cc_final: 0.8152 (tt) REVERT: A 526 GLU cc_start: 0.8475 (pt0) cc_final: 0.8231 (tm-30) REVERT: A 571 MET cc_start: 0.8156 (mtm) cc_final: 0.7504 (mtp) REVERT: A 578 ILE cc_start: 0.9112 (mm) cc_final: 0.8557 (tt) REVERT: A 582 PHE cc_start: 0.8389 (m-80) cc_final: 0.8117 (m-80) REVERT: A 623 MET cc_start: 0.9040 (tpp) cc_final: 0.8791 (tpp) REVERT: A 808 LEU cc_start: 0.9558 (tt) cc_final: 0.9005 (pp) REVERT: A 843 MET cc_start: 0.8730 (mpp) cc_final: 0.8282 (mpp) REVERT: A 879 LEU cc_start: 0.9321 (mm) cc_final: 0.8992 (mm) REVERT: A 902 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8518 (mttt) REVERT: B 334 LEU cc_start: 0.9431 (tp) cc_final: 0.9182 (tt) REVERT: B 377 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8564 (mmtm) REVERT: B 417 ASP cc_start: 0.7470 (t0) cc_final: 0.5536 (p0) REVERT: B 437 PHE cc_start: 0.8638 (t80) cc_final: 0.8435 (t80) REVERT: B 440 MET cc_start: 0.8648 (tmm) cc_final: 0.8389 (tmm) REVERT: B 458 HIS cc_start: 0.8277 (t-90) cc_final: 0.8027 (t-90) REVERT: B 460 TYR cc_start: 0.9124 (m-10) cc_final: 0.8787 (m-10) REVERT: B 496 MET cc_start: 0.7068 (ppp) cc_final: 0.5546 (tmm) REVERT: B 547 ARG cc_start: 0.3748 (tmt-80) cc_final: 0.3180 (ptm160) REVERT: B 604 TYR cc_start: 0.7469 (m-10) cc_final: 0.6982 (m-10) REVERT: C 111 ASP cc_start: 0.8926 (m-30) cc_final: 0.8397 (p0) REVERT: C 113 THR cc_start: 0.7421 (p) cc_final: 0.6878 (p) REVERT: C 198 ASP cc_start: 0.9248 (p0) cc_final: 0.8889 (p0) REVERT: C 206 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8667 (mttp) REVERT: C 213 PHE cc_start: 0.8903 (m-80) cc_final: 0.8697 (m-80) REVERT: C 214 ASN cc_start: 0.8523 (p0) cc_final: 0.8232 (t0) REVERT: C 361 MET cc_start: 0.9024 (ptp) cc_final: 0.8562 (ptp) REVERT: C 428 TYR cc_start: 0.8474 (t80) cc_final: 0.8242 (t80) REVERT: C 498 LEU cc_start: 0.9251 (mm) cc_final: 0.9005 (mm) REVERT: C 523 GLN cc_start: 0.8182 (pt0) cc_final: 0.7820 (pt0) REVERT: C 540 PHE cc_start: 0.8647 (t80) cc_final: 0.8246 (t80) REVERT: E 183 CYS cc_start: 0.8769 (m) cc_final: 0.8527 (t) REVERT: E 195 ASP cc_start: 0.9112 (p0) cc_final: 0.8781 (p0) REVERT: E 324 LEU cc_start: 0.7858 (pt) cc_final: 0.7468 (pt) REVERT: D 90 ILE cc_start: 0.9189 (tt) cc_final: 0.8919 (pt) REVERT: D 123 TYR cc_start: 0.8874 (m-80) cc_final: 0.8548 (m-80) REVERT: D 240 HIS cc_start: 0.8428 (m90) cc_final: 0.8192 (t-170) REVERT: D 253 LYS cc_start: 0.8795 (mmtt) cc_final: 0.7880 (mtmt) REVERT: D 259 TYR cc_start: 0.9095 (m-10) cc_final: 0.8561 (m-10) REVERT: D 262 LYS cc_start: 0.8498 (tmtt) cc_final: 0.7898 (tptp) REVERT: D 268 PHE cc_start: 0.8982 (t80) cc_final: 0.8465 (t80) REVERT: D 270 GLN cc_start: 0.9168 (mm110) cc_final: 0.8830 (tm-30) REVERT: D 365 ASP cc_start: 0.7972 (m-30) cc_final: 0.7734 (m-30) REVERT: D 425 ARG cc_start: 0.8256 (ptt90) cc_final: 0.7844 (tpt90) REVERT: D 467 ASP cc_start: 0.8024 (m-30) cc_final: 0.7560 (m-30) REVERT: D 512 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7764 (mm-30) REVERT: F 350 MET cc_start: 0.9413 (tmm) cc_final: 0.9169 (tmm) REVERT: F 354 MET cc_start: 0.8435 (mmp) cc_final: 0.8049 (mmp) REVERT: F 356 THR cc_start: 0.6381 (p) cc_final: 0.6168 (p) REVERT: F 364 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8615 (mp0) REVERT: F 410 ASN cc_start: 0.8709 (t0) cc_final: 0.8460 (t0) REVERT: 3 920 PHE cc_start: 0.8330 (m-80) cc_final: 0.7716 (m-80) REVERT: 3 945 MET cc_start: 0.9581 (ttp) cc_final: 0.9320 (tpp) REVERT: 7 776 MET cc_start: 0.4766 (pmm) cc_final: 0.4477 (pmm) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3507 time to fit residues: 278.3219 Evaluate side-chains 390 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 chunk 200 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 273 optimal weight: 0.0270 chunk 171 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 63 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 82 GLN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25231 Z= 0.161 Angle : 0.591 9.501 34442 Z= 0.304 Chirality : 0.041 0.199 3957 Planarity : 0.004 0.061 4024 Dihedral : 16.916 132.574 4026 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2738 helix: -0.62 (0.13), residues: 1435 sheet: -0.90 (0.34), residues: 239 loop : -1.48 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 585 HIS 0.006 0.001 HIS A 777 PHE 0.038 0.001 PHE B 475 TYR 0.024 0.001 TYR E 473 ARG 0.008 0.000 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8763 (mmp) cc_final: 0.8411 (mmm) REVERT: 9 184 LYS cc_start: 0.9429 (mptt) cc_final: 0.9204 (mmtt) REVERT: 9 222 LEU cc_start: 0.9576 (tp) cc_final: 0.9295 (tp) REVERT: 9 224 GLU cc_start: 0.7339 (tp30) cc_final: 0.7127 (tp30) REVERT: 9 261 MET cc_start: 0.7992 (mpp) cc_final: 0.7557 (mpp) REVERT: 9 296 MET cc_start: 0.6087 (mtt) cc_final: 0.5580 (mmt) REVERT: 9 315 MET cc_start: 0.8743 (tmm) cc_final: 0.8474 (tmm) REVERT: 9 322 LYS cc_start: 0.8564 (mttp) cc_final: 0.7637 (tttt) REVERT: 9 419 CYS cc_start: 0.9389 (t) cc_final: 0.8562 (t) REVERT: 9 423 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8329 (tp-100) REVERT: 9 432 THR cc_start: 0.9482 (p) cc_final: 0.8753 (p) REVERT: 9 435 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8472 (pt0) REVERT: 9 499 TYR cc_start: 0.8872 (m-10) cc_final: 0.8326 (m-80) REVERT: 9 511 PHE cc_start: 0.7808 (t80) cc_final: 0.7520 (t80) REVERT: A 411 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7857 (mttp) REVERT: A 513 ILE cc_start: 0.8621 (mm) cc_final: 0.8163 (tt) REVERT: A 526 GLU cc_start: 0.8454 (pt0) cc_final: 0.8238 (tm-30) REVERT: A 571 MET cc_start: 0.8106 (mtm) cc_final: 0.7430 (mtp) REVERT: A 578 ILE cc_start: 0.9141 (mm) cc_final: 0.8518 (tt) REVERT: A 808 LEU cc_start: 0.9559 (tt) cc_final: 0.9021 (pp) REVERT: A 843 MET cc_start: 0.8824 (mpp) cc_final: 0.8387 (mpp) REVERT: A 879 LEU cc_start: 0.9346 (mm) cc_final: 0.9037 (mm) REVERT: A 902 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8520 (mttt) REVERT: B 334 LEU cc_start: 0.9423 (tp) cc_final: 0.9196 (tt) REVERT: B 377 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8558 (mmtm) REVERT: B 417 ASP cc_start: 0.7409 (t0) cc_final: 0.5522 (p0) REVERT: B 437 PHE cc_start: 0.8733 (t80) cc_final: 0.8405 (t80) REVERT: B 440 MET cc_start: 0.8660 (tmm) cc_final: 0.8359 (tmm) REVERT: B 444 LEU cc_start: 0.9413 (mt) cc_final: 0.8986 (mt) REVERT: B 458 HIS cc_start: 0.8259 (t-90) cc_final: 0.7778 (t70) REVERT: B 460 TYR cc_start: 0.9106 (m-10) cc_final: 0.8735 (m-10) REVERT: B 465 TRP cc_start: 0.8799 (m-90) cc_final: 0.8255 (m-90) REVERT: B 496 MET cc_start: 0.6806 (ppp) cc_final: 0.5352 (tmm) REVERT: B 547 ARG cc_start: 0.3817 (tmt-80) cc_final: 0.3047 (ptm160) REVERT: B 604 TYR cc_start: 0.7444 (m-10) cc_final: 0.6963 (m-10) REVERT: C 111 ASP cc_start: 0.8924 (m-30) cc_final: 0.8677 (m-30) REVERT: C 198 ASP cc_start: 0.9274 (p0) cc_final: 0.8869 (p0) REVERT: C 206 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8715 (mttp) REVERT: C 214 ASN cc_start: 0.8580 (p0) cc_final: 0.8266 (t0) REVERT: C 321 LEU cc_start: 0.9590 (mp) cc_final: 0.9321 (mm) REVERT: C 361 MET cc_start: 0.9027 (ptp) cc_final: 0.8573 (ptp) REVERT: C 428 TYR cc_start: 0.8577 (t80) cc_final: 0.8310 (t80) REVERT: C 498 LEU cc_start: 0.9273 (mm) cc_final: 0.8596 (mm) REVERT: C 523 GLN cc_start: 0.8165 (pt0) cc_final: 0.7782 (pt0) REVERT: C 540 PHE cc_start: 0.8640 (t80) cc_final: 0.8235 (t80) REVERT: C 585 MET cc_start: 0.6946 (ttt) cc_final: 0.5721 (tmm) REVERT: E 79 ARG cc_start: 0.8859 (ptp90) cc_final: 0.8484 (ptp-170) REVERT: E 183 CYS cc_start: 0.8622 (m) cc_final: 0.8138 (t) REVERT: E 195 ASP cc_start: 0.9120 (p0) cc_final: 0.8776 (p0) REVERT: E 210 MET cc_start: 0.8505 (mmp) cc_final: 0.8136 (mmt) REVERT: E 324 LEU cc_start: 0.7778 (pt) cc_final: 0.7437 (pt) REVERT: D 90 ILE cc_start: 0.9278 (tt) cc_final: 0.9030 (pt) REVERT: D 123 TYR cc_start: 0.8873 (m-80) cc_final: 0.8584 (m-80) REVERT: D 240 HIS cc_start: 0.8437 (m90) cc_final: 0.8224 (t-170) REVERT: D 253 LYS cc_start: 0.8771 (mmtt) cc_final: 0.7861 (mtmt) REVERT: D 259 TYR cc_start: 0.9083 (m-10) cc_final: 0.8577 (m-10) REVERT: D 262 LYS cc_start: 0.8477 (tmtt) cc_final: 0.7809 (tptp) REVERT: D 268 PHE cc_start: 0.8996 (t80) cc_final: 0.8467 (t80) REVERT: D 270 GLN cc_start: 0.9108 (mm110) cc_final: 0.8705 (tm-30) REVERT: D 365 ASP cc_start: 0.7988 (m-30) cc_final: 0.7734 (m-30) REVERT: D 425 ARG cc_start: 0.8288 (ptt90) cc_final: 0.7874 (tpt90) REVERT: D 467 ASP cc_start: 0.8157 (m-30) cc_final: 0.7658 (m-30) REVERT: D 512 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7883 (mm-30) REVERT: F 350 MET cc_start: 0.9432 (tmm) cc_final: 0.9221 (tmm) REVERT: F 354 MET cc_start: 0.8464 (mmp) cc_final: 0.8075 (mmp) REVERT: F 356 THR cc_start: 0.6408 (p) cc_final: 0.6200 (p) REVERT: F 364 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8618 (mp0) REVERT: F 378 TRP cc_start: 0.7748 (p-90) cc_final: 0.7451 (p-90) REVERT: F 410 ASN cc_start: 0.8656 (t0) cc_final: 0.8416 (t0) REVERT: 3 920 PHE cc_start: 0.8352 (m-80) cc_final: 0.7802 (m-80) REVERT: 3 945 MET cc_start: 0.9588 (ttp) cc_final: 0.9333 (tpp) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.3486 time to fit residues: 272.1383 Evaluate side-chains 383 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 198 GLN ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 63 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25231 Z= 0.155 Angle : 0.582 10.493 34442 Z= 0.299 Chirality : 0.041 0.198 3957 Planarity : 0.003 0.060 4024 Dihedral : 16.830 131.082 4026 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2738 helix: -0.48 (0.14), residues: 1428 sheet: -0.91 (0.35), residues: 227 loop : -1.40 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 585 HIS 0.005 0.001 HIS C 69 PHE 0.035 0.001 PHE B 475 TYR 0.017 0.001 TYR B 473 ARG 0.007 0.000 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8713 (mmp) cc_final: 0.8501 (mmm) REVERT: 9 184 LYS cc_start: 0.9443 (mptt) cc_final: 0.9201 (mmtt) REVERT: 9 222 LEU cc_start: 0.9551 (tp) cc_final: 0.9215 (tp) REVERT: 9 244 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8042 (pt0) REVERT: 9 261 MET cc_start: 0.7858 (mpp) cc_final: 0.7313 (mpp) REVERT: 9 296 MET cc_start: 0.6131 (mtt) cc_final: 0.5698 (mmt) REVERT: 9 322 LYS cc_start: 0.8594 (mttp) cc_final: 0.7712 (tttt) REVERT: 9 323 LYS cc_start: 0.8639 (mmpt) cc_final: 0.8301 (mmmt) REVERT: 9 419 CYS cc_start: 0.9383 (t) cc_final: 0.8566 (t) REVERT: 9 423 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8422 (tp-100) REVERT: 9 432 THR cc_start: 0.9438 (p) cc_final: 0.8802 (p) REVERT: 9 435 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8316 (pt0) REVERT: 9 499 TYR cc_start: 0.8880 (m-10) cc_final: 0.8348 (m-80) REVERT: 9 511 PHE cc_start: 0.7816 (t80) cc_final: 0.7523 (t80) REVERT: A 411 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7916 (mttp) REVERT: A 513 ILE cc_start: 0.8611 (mm) cc_final: 0.8157 (tt) REVERT: A 571 MET cc_start: 0.8096 (mtm) cc_final: 0.7415 (mtp) REVERT: A 578 ILE cc_start: 0.9066 (mm) cc_final: 0.8365 (tt) REVERT: A 623 MET cc_start: 0.9141 (tpp) cc_final: 0.8708 (tmm) REVERT: A 808 LEU cc_start: 0.9556 (tt) cc_final: 0.9138 (pp) REVERT: A 843 MET cc_start: 0.8825 (mpp) cc_final: 0.8373 (mpp) REVERT: A 879 LEU cc_start: 0.9360 (mm) cc_final: 0.9070 (mm) REVERT: A 902 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8499 (mttt) REVERT: B 334 LEU cc_start: 0.9422 (tp) cc_final: 0.9210 (tt) REVERT: B 377 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8817 (ptpp) REVERT: B 417 ASP cc_start: 0.7387 (t0) cc_final: 0.5423 (p0) REVERT: B 437 PHE cc_start: 0.8747 (t80) cc_final: 0.8449 (t80) REVERT: B 440 MET cc_start: 0.8661 (tmm) cc_final: 0.8344 (tmm) REVERT: B 444 LEU cc_start: 0.9407 (mt) cc_final: 0.8952 (mt) REVERT: B 458 HIS cc_start: 0.8269 (t-90) cc_final: 0.7783 (t70) REVERT: B 460 TYR cc_start: 0.9102 (m-10) cc_final: 0.8757 (m-10) REVERT: B 465 TRP cc_start: 0.8849 (m-90) cc_final: 0.8078 (m-90) REVERT: B 471 GLN cc_start: 0.8664 (tt0) cc_final: 0.8327 (tm-30) REVERT: B 496 MET cc_start: 0.6719 (ppp) cc_final: 0.5164 (tmm) REVERT: B 547 ARG cc_start: 0.3748 (tmt-80) cc_final: 0.3033 (ptm160) REVERT: B 604 TYR cc_start: 0.7361 (m-10) cc_final: 0.6801 (m-10) REVERT: C 198 ASP cc_start: 0.9262 (p0) cc_final: 0.8860 (p0) REVERT: C 206 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8678 (mttp) REVERT: C 213 PHE cc_start: 0.8824 (m-80) cc_final: 0.8498 (m-10) REVERT: C 214 ASN cc_start: 0.8560 (p0) cc_final: 0.8232 (t0) REVERT: C 361 MET cc_start: 0.9021 (ptp) cc_final: 0.8464 (mpp) REVERT: C 428 TYR cc_start: 0.8511 (t80) cc_final: 0.8231 (t80) REVERT: C 498 LEU cc_start: 0.9268 (mm) cc_final: 0.8512 (mm) REVERT: C 523 GLN cc_start: 0.8125 (pt0) cc_final: 0.7759 (pt0) REVERT: C 540 PHE cc_start: 0.8630 (t80) cc_final: 0.8220 (t80) REVERT: C 585 MET cc_start: 0.6859 (ttt) cc_final: 0.5583 (tmm) REVERT: E 79 ARG cc_start: 0.8850 (ptp90) cc_final: 0.8456 (ptp-170) REVERT: E 210 MET cc_start: 0.8547 (mmp) cc_final: 0.8152 (mmt) REVERT: D 90 ILE cc_start: 0.9295 (tt) cc_final: 0.9042 (pt) REVERT: D 123 TYR cc_start: 0.8810 (m-80) cc_final: 0.8584 (m-80) REVERT: D 253 LYS cc_start: 0.8754 (mmtt) cc_final: 0.7853 (mtmt) REVERT: D 259 TYR cc_start: 0.9073 (m-10) cc_final: 0.8527 (m-10) REVERT: D 262 LYS cc_start: 0.8339 (tmtt) cc_final: 0.7691 (tptp) REVERT: D 268 PHE cc_start: 0.8974 (t80) cc_final: 0.8469 (t80) REVERT: D 270 GLN cc_start: 0.9163 (mm110) cc_final: 0.8767 (tm-30) REVERT: D 365 ASP cc_start: 0.8143 (m-30) cc_final: 0.7881 (m-30) REVERT: D 425 ARG cc_start: 0.8293 (ptt90) cc_final: 0.7876 (tpt90) REVERT: D 467 ASP cc_start: 0.8187 (m-30) cc_final: 0.7663 (m-30) REVERT: D 512 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7861 (mm-30) REVERT: F 332 PHE cc_start: 0.9197 (m-80) cc_final: 0.8982 (m-80) REVERT: F 364 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8620 (mp0) REVERT: F 385 ARG cc_start: 0.8982 (tpm170) cc_final: 0.8574 (tpm170) REVERT: F 410 ASN cc_start: 0.8669 (t0) cc_final: 0.8149 (t0) REVERT: 3 920 PHE cc_start: 0.8346 (m-80) cc_final: 0.7843 (m-80) REVERT: 3 945 MET cc_start: 0.9557 (ttp) cc_final: 0.9306 (tpp) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3762 time to fit residues: 297.6514 Evaluate side-chains 376 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 198 GLN ** 9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25231 Z= 0.238 Angle : 0.638 11.765 34442 Z= 0.333 Chirality : 0.042 0.221 3957 Planarity : 0.004 0.072 4024 Dihedral : 16.842 132.576 4026 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2738 helix: -0.48 (0.13), residues: 1430 sheet: -0.75 (0.35), residues: 219 loop : -1.34 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 529 HIS 0.008 0.001 HIS D 240 PHE 0.032 0.002 PHE B 475 TYR 0.020 0.001 TYR B 473 ARG 0.010 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8738 (mmp) cc_final: 0.8439 (mmm) REVERT: 9 184 LYS cc_start: 0.9484 (mptt) cc_final: 0.9258 (mmtt) REVERT: 9 222 LEU cc_start: 0.9591 (tp) cc_final: 0.9199 (tp) REVERT: 9 225 MET cc_start: 0.8464 (ttp) cc_final: 0.8035 (ptm) REVERT: 9 261 MET cc_start: 0.8002 (mpp) cc_final: 0.6613 (mpp) REVERT: 9 322 LYS cc_start: 0.8649 (mttp) cc_final: 0.7906 (tttt) REVERT: 9 323 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8136 (mmmt) REVERT: 9 432 THR cc_start: 0.9539 (p) cc_final: 0.8974 (p) REVERT: 9 435 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8400 (pt0) REVERT: 9 499 TYR cc_start: 0.8971 (m-10) cc_final: 0.8441 (m-80) REVERT: A 411 LYS cc_start: 0.8484 (mmmt) cc_final: 0.7952 (mttp) REVERT: A 513 ILE cc_start: 0.8651 (mm) cc_final: 0.8200 (tt) REVERT: A 571 MET cc_start: 0.8235 (mtm) cc_final: 0.7419 (mtt) REVERT: A 578 ILE cc_start: 0.9195 (mm) cc_final: 0.8800 (tt) REVERT: A 582 PHE cc_start: 0.8377 (m-80) cc_final: 0.8051 (m-80) REVERT: A 808 LEU cc_start: 0.9491 (tt) cc_final: 0.9001 (pp) REVERT: A 843 MET cc_start: 0.8837 (mpp) cc_final: 0.8379 (mpp) REVERT: A 879 LEU cc_start: 0.9372 (mm) cc_final: 0.9001 (mm) REVERT: A 902 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8515 (mttt) REVERT: B 300 MET cc_start: 0.9050 (ttp) cc_final: 0.8836 (ttm) REVERT: B 377 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8577 (mmtm) REVERT: B 417 ASP cc_start: 0.7572 (t0) cc_final: 0.5323 (p0) REVERT: B 440 MET cc_start: 0.8736 (tmm) cc_final: 0.8414 (tmm) REVERT: B 444 LEU cc_start: 0.9446 (mt) cc_final: 0.8896 (mt) REVERT: B 458 HIS cc_start: 0.8435 (t-90) cc_final: 0.7864 (t70) REVERT: B 460 TYR cc_start: 0.9086 (m-10) cc_final: 0.8788 (m-10) REVERT: B 465 TRP cc_start: 0.8890 (m-90) cc_final: 0.8093 (m-90) REVERT: B 466 ASP cc_start: 0.8805 (p0) cc_final: 0.8587 (p0) REVERT: B 471 GLN cc_start: 0.8790 (tt0) cc_final: 0.8442 (tm-30) REVERT: B 496 MET cc_start: 0.6826 (ppp) cc_final: 0.5297 (tmm) REVERT: B 547 ARG cc_start: 0.3960 (tmt-80) cc_final: 0.3485 (ptm160) REVERT: B 561 HIS cc_start: 0.9122 (m90) cc_final: 0.8205 (t-170) REVERT: B 604 TYR cc_start: 0.7430 (m-10) cc_final: 0.6985 (m-10) REVERT: C 111 ASP cc_start: 0.8811 (m-30) cc_final: 0.8263 (p0) REVERT: C 113 THR cc_start: 0.7625 (p) cc_final: 0.7146 (p) REVERT: C 206 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8697 (mttp) REVERT: C 213 PHE cc_start: 0.8983 (m-80) cc_final: 0.8701 (m-10) REVERT: C 214 ASN cc_start: 0.8600 (p0) cc_final: 0.8317 (t0) REVERT: C 361 MET cc_start: 0.9032 (ptp) cc_final: 0.8618 (ptp) REVERT: C 423 ASN cc_start: 0.9534 (t0) cc_final: 0.8635 (t0) REVERT: C 428 TYR cc_start: 0.8591 (t80) cc_final: 0.8292 (t80) REVERT: C 498 LEU cc_start: 0.9283 (mm) cc_final: 0.8611 (mm) REVERT: C 523 GLN cc_start: 0.8231 (pt0) cc_final: 0.7771 (pt0) REVERT: C 540 PHE cc_start: 0.8662 (t80) cc_final: 0.8255 (t80) REVERT: C 585 MET cc_start: 0.6921 (ttt) cc_final: 0.5570 (tmm) REVERT: E 79 ARG cc_start: 0.8911 (ptp90) cc_final: 0.8500 (ptp-170) REVERT: E 170 MET cc_start: 0.8694 (ptp) cc_final: 0.8472 (ptp) REVERT: E 210 MET cc_start: 0.8606 (mmp) cc_final: 0.8396 (mmt) REVERT: E 324 LEU cc_start: 0.7959 (pt) cc_final: 0.7501 (pt) REVERT: D 76 GLN cc_start: 0.9043 (mt0) cc_final: 0.8737 (tm-30) REVERT: D 123 TYR cc_start: 0.8984 (m-80) cc_final: 0.8613 (m-80) REVERT: D 259 TYR cc_start: 0.9088 (m-10) cc_final: 0.8728 (m-10) REVERT: D 268 PHE cc_start: 0.9061 (t80) cc_final: 0.8517 (t80) REVERT: D 270 GLN cc_start: 0.9216 (mm110) cc_final: 0.8892 (tm-30) REVERT: D 365 ASP cc_start: 0.8081 (m-30) cc_final: 0.7769 (m-30) REVERT: D 425 ARG cc_start: 0.8395 (ptt90) cc_final: 0.8009 (tpt90) REVERT: D 467 ASP cc_start: 0.8259 (m-30) cc_final: 0.7751 (m-30) REVERT: D 512 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7894 (mm-30) REVERT: F 332 PHE cc_start: 0.9207 (m-80) cc_final: 0.8959 (m-80) REVERT: F 350 MET cc_start: 0.9465 (tmm) cc_final: 0.9182 (tmm) REVERT: F 364 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8629 (mp0) REVERT: F 378 TRP cc_start: 0.8016 (p-90) cc_final: 0.7619 (p-90) REVERT: F 385 ARG cc_start: 0.9036 (tpm170) cc_final: 0.8617 (tpm170) REVERT: F 410 ASN cc_start: 0.8769 (t0) cc_final: 0.8459 (t0) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.3615 time to fit residues: 269.5076 Evaluate side-chains 363 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 187 optimal weight: 0.0000 chunk 282 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 198 GLN ** 9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 413 GLN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN D 240 HIS ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 950 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25231 Z= 0.152 Angle : 0.611 14.168 34442 Z= 0.310 Chirality : 0.042 0.175 3957 Planarity : 0.004 0.064 4024 Dihedral : 16.755 129.071 4026 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2738 helix: -0.36 (0.14), residues: 1425 sheet: -0.71 (0.36), residues: 215 loop : -1.33 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 585 HIS 0.015 0.001 HIS D 240 PHE 0.028 0.001 PHE B 475 TYR 0.017 0.001 TYR B 473 ARG 0.010 0.000 ARG 9 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8745 (mmp) cc_final: 0.8542 (mmm) REVERT: 9 222 LEU cc_start: 0.9512 (tp) cc_final: 0.9243 (tp) REVERT: 9 259 ILE cc_start: 0.8982 (mp) cc_final: 0.8721 (mp) REVERT: 9 261 MET cc_start: 0.7897 (mpp) cc_final: 0.7580 (mpp) REVERT: 9 296 MET cc_start: 0.6077 (mtt) cc_final: 0.5660 (mmt) REVERT: 9 419 CYS cc_start: 0.9324 (t) cc_final: 0.8661 (t) REVERT: 9 423 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8828 (tp-100) REVERT: 9 432 THR cc_start: 0.9459 (p) cc_final: 0.8909 (p) REVERT: 9 435 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8329 (pt0) REVERT: 9 499 TYR cc_start: 0.8926 (m-10) cc_final: 0.8376 (m-80) REVERT: 9 511 PHE cc_start: 0.7935 (t80) cc_final: 0.7704 (t80) REVERT: A 411 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7999 (mttp) REVERT: A 513 ILE cc_start: 0.8616 (mm) cc_final: 0.8171 (tt) REVERT: A 571 MET cc_start: 0.8218 (mtm) cc_final: 0.7291 (mtp) REVERT: A 578 ILE cc_start: 0.9070 (mm) cc_final: 0.8377 (tt) REVERT: A 579 MET cc_start: 0.8904 (mmp) cc_final: 0.8696 (mmp) REVERT: A 582 PHE cc_start: 0.8252 (m-80) cc_final: 0.7775 (m-80) REVERT: A 623 MET cc_start: 0.9186 (tpp) cc_final: 0.8416 (tmm) REVERT: A 808 LEU cc_start: 0.9488 (tt) cc_final: 0.9052 (pp) REVERT: A 843 MET cc_start: 0.8855 (mpp) cc_final: 0.8400 (mpp) REVERT: A 879 LEU cc_start: 0.9394 (mm) cc_final: 0.8974 (mm) REVERT: A 902 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8552 (mttt) REVERT: B 376 PHE cc_start: 0.8790 (t80) cc_final: 0.8567 (t80) REVERT: B 377 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8600 (mmtm) REVERT: B 417 ASP cc_start: 0.7492 (t0) cc_final: 0.5529 (p0) REVERT: B 437 PHE cc_start: 0.8714 (t80) cc_final: 0.8452 (t80) REVERT: B 440 MET cc_start: 0.8655 (tmm) cc_final: 0.8347 (tmm) REVERT: B 444 LEU cc_start: 0.9410 (mt) cc_final: 0.8938 (mt) REVERT: B 458 HIS cc_start: 0.8310 (t-90) cc_final: 0.7827 (t70) REVERT: B 460 TYR cc_start: 0.9014 (m-10) cc_final: 0.8754 (m-10) REVERT: B 465 TRP cc_start: 0.8724 (m-90) cc_final: 0.7982 (m-90) REVERT: B 471 GLN cc_start: 0.8714 (tt0) cc_final: 0.8350 (tm-30) REVERT: B 496 MET cc_start: 0.6689 (ppp) cc_final: 0.5144 (tmm) REVERT: B 547 ARG cc_start: 0.3865 (tmt-80) cc_final: 0.3403 (ptm160) REVERT: B 561 HIS cc_start: 0.9033 (m90) cc_final: 0.8274 (t-170) REVERT: B 604 TYR cc_start: 0.7367 (m-10) cc_final: 0.6907 (m-10) REVERT: C 73 ASP cc_start: 0.8806 (m-30) cc_final: 0.8327 (p0) REVERT: C 111 ASP cc_start: 0.8821 (m-30) cc_final: 0.8319 (p0) REVERT: C 113 THR cc_start: 0.7601 (p) cc_final: 0.7214 (p) REVERT: C 198 ASP cc_start: 0.9247 (p0) cc_final: 0.8861 (p0) REVERT: C 206 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8692 (mttp) REVERT: C 213 PHE cc_start: 0.8930 (m-80) cc_final: 0.8642 (m-10) REVERT: C 214 ASN cc_start: 0.8492 (p0) cc_final: 0.8258 (t0) REVERT: C 361 MET cc_start: 0.9003 (ptp) cc_final: 0.8472 (mpp) REVERT: C 423 ASN cc_start: 0.9520 (t0) cc_final: 0.8512 (t0) REVERT: C 428 TYR cc_start: 0.8624 (t80) cc_final: 0.8334 (t80) REVERT: C 498 LEU cc_start: 0.9283 (mm) cc_final: 0.8561 (mm) REVERT: C 523 GLN cc_start: 0.8201 (pt0) cc_final: 0.7816 (pt0) REVERT: C 540 PHE cc_start: 0.8600 (t80) cc_final: 0.8182 (t80) REVERT: C 585 MET cc_start: 0.6922 (ttt) cc_final: 0.5446 (tmm) REVERT: E 63 GLU cc_start: 0.8331 (tp30) cc_final: 0.8042 (tp30) REVERT: E 79 ARG cc_start: 0.8837 (ptp90) cc_final: 0.8430 (ptp-170) REVERT: E 210 MET cc_start: 0.8522 (mmp) cc_final: 0.8135 (mmt) REVERT: E 324 LEU cc_start: 0.7878 (pt) cc_final: 0.7428 (pt) REVERT: D 90 ILE cc_start: 0.9199 (tt) cc_final: 0.8979 (pt) REVERT: D 123 TYR cc_start: 0.8838 (m-80) cc_final: 0.8536 (m-80) REVERT: D 248 PHE cc_start: 0.8986 (m-80) cc_final: 0.8779 (m-80) REVERT: D 253 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8000 (mtmt) REVERT: D 259 TYR cc_start: 0.9061 (m-10) cc_final: 0.8371 (m-10) REVERT: D 262 LYS cc_start: 0.8315 (tmtt) cc_final: 0.7662 (tptp) REVERT: D 268 PHE cc_start: 0.8985 (t80) cc_final: 0.8490 (t80) REVERT: D 270 GLN cc_start: 0.9200 (mm110) cc_final: 0.8823 (tm-30) REVERT: D 365 ASP cc_start: 0.8056 (m-30) cc_final: 0.7789 (m-30) REVERT: D 425 ARG cc_start: 0.8374 (ptt90) cc_final: 0.7966 (tpt90) REVERT: D 467 ASP cc_start: 0.8259 (m-30) cc_final: 0.7711 (m-30) REVERT: D 512 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7848 (mm-30) REVERT: F 332 PHE cc_start: 0.9200 (m-80) cc_final: 0.8956 (m-80) REVERT: F 350 MET cc_start: 0.9443 (tmm) cc_final: 0.9206 (tmm) REVERT: F 364 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8683 (mp0) REVERT: F 378 TRP cc_start: 0.8038 (p-90) cc_final: 0.7679 (p-90) REVERT: F 385 ARG cc_start: 0.9006 (tpm170) cc_final: 0.8588 (tpm170) REVERT: F 410 ASN cc_start: 0.8831 (t0) cc_final: 0.8518 (t0) REVERT: 3 903 LEU cc_start: 0.8817 (mm) cc_final: 0.8528 (mm) REVERT: 3 906 THR cc_start: 0.8295 (p) cc_final: 0.7994 (p) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.3605 time to fit residues: 279.2839 Evaluate side-chains 378 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 198 GLN ** 9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.103516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.079706 restraints weight = 98835.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081674 restraints weight = 61978.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.083025 restraints weight = 43979.009| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25231 Z= 0.162 Angle : 0.617 10.084 34442 Z= 0.315 Chirality : 0.041 0.196 3957 Planarity : 0.004 0.060 4024 Dihedral : 16.699 127.043 4026 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2738 helix: -0.31 (0.14), residues: 1425 sheet: -0.71 (0.36), residues: 217 loop : -1.34 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP 3 959 HIS 0.012 0.001 HIS D 240 PHE 0.025 0.001 PHE B 475 TYR 0.016 0.001 TYR B 473 ARG 0.009 0.000 ARG D 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5576.14 seconds wall clock time: 102 minutes 23.93 seconds (6143.93 seconds total)