Starting phenix.real_space_refine on Sat Mar 23 03:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhv_9119/03_2024/6mhv_9119.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 S 100 5.16 5 C 12052 2.51 5 N 3096 2.21 5 O 3096 1.98 5 H 17152 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 714": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 714": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 714": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 714": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35496 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8874 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 30, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 278 Chain: "C" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8874 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 30, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 278 Chain: "A" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8874 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 30, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 278 Chain: "D" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8874 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 30, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 278 Time building chain proxies: 15.50, per 1000 atoms: 0.44 Number of scatterers: 35496 At special positions: 0 Unit cell: (139.15, 139.15, 128.8, 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 100 16.00 O 3096 8.00 N 3096 7.00 C 12052 6.00 H 17152 1.00 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: 25.70 Conformation dependent library (CDL) restraints added in 4.1 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 8 sheets defined 67.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.513A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.570A pdb=" N GLN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.696A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 481 through 508 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.515A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 3.620A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.809A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.538A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.788A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.786A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 707 removed outlier: 3.817A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 133 through 148 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.513A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.570A pdb=" N GLN C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.696A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 481 through 508 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.515A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 3.619A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.809A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.538A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.787A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.786A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 707 removed outlier: 3.816A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 133 through 148 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.513A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.571A pdb=" N GLN A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 481 through 508 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.514A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 3.620A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.809A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.539A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.787A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.786A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.816A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.512A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.571A pdb=" N GLN D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.696A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 481 through 508 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.514A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 3.621A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.808A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.538A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.788A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.786A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 707 removed outlier: 3.817A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 380 removed outlier: 7.083A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'C' and resid 376 through 380 removed outlier: 7.084A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 380 removed outlier: 7.082A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 380 removed outlier: 7.083A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1161 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.27 Time building geometry restraints manager: 26.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17124 1.03 - 1.22: 69 1.22 - 1.42: 7811 1.42 - 1.61: 10728 1.61 - 1.81: 168 Bond restraints: 35900 Sorted by residual: bond pdb=" SG CYS D 171 " pdb=" HG CYS D 171 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" SG CYS B 171 " pdb=" HG CYS B 171 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS A 171 " pdb=" HG CYS A 171 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS C 171 " pdb=" HG CYS C 171 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" N ASP B 726 " pdb=" CA ASP B 726 " ideal model delta sigma weight residual 1.459 1.515 -0.056 1.32e-02 5.74e+03 1.81e+01 ... (remaining 35895 not shown) Histogram of bond angle deviations from ideal: 65.31 - 80.82: 8 80.82 - 96.32: 48 96.32 - 111.83: 39619 111.83 - 127.33: 24545 127.33 - 142.83: 216 Bond angle restraints: 64436 Sorted by residual: angle pdb=" C GLU C 725 " pdb=" N ASP C 726 " pdb=" H ASP C 726 " ideal model delta sigma weight residual 122.99 65.31 57.68 3.00e+00 1.11e-01 3.70e+02 angle pdb=" C GLU D 725 " pdb=" N ASP D 726 " pdb=" H ASP D 726 " ideal model delta sigma weight residual 122.99 65.35 57.64 3.00e+00 1.11e-01 3.69e+02 angle pdb=" C GLU A 725 " pdb=" N ASP A 726 " pdb=" H ASP A 726 " ideal model delta sigma weight residual 122.99 65.36 57.64 3.00e+00 1.11e-01 3.69e+02 angle pdb=" C GLU B 725 " pdb=" N ASP B 726 " pdb=" H ASP B 726 " ideal model delta sigma weight residual 122.99 65.38 57.61 3.00e+00 1.11e-01 3.69e+02 angle pdb=" CA ASP B 726 " pdb=" N ASP B 726 " pdb=" H ASP B 726 " ideal model delta sigma weight residual 112.69 77.56 35.14 3.00e+00 1.11e-01 1.37e+02 ... (remaining 64431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.86: 15448 11.86 - 23.73: 1319 23.73 - 35.59: 221 35.59 - 47.45: 92 47.45 - 59.32: 116 Dihedral angle restraints: 17196 sinusoidal: 8520 harmonic: 8676 Sorted by residual: dihedral pdb=" N ASP C 726 " pdb=" C ASP C 726 " pdb=" CA ASP C 726 " pdb=" CB ASP C 726 " ideal model delta harmonic sigma weight residual 122.80 134.25 -11.45 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" N ASP A 726 " pdb=" C ASP A 726 " pdb=" CA ASP A 726 " pdb=" CB ASP A 726 " ideal model delta harmonic sigma weight residual 122.80 134.24 -11.44 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" N ASP D 726 " pdb=" C ASP D 726 " pdb=" CA ASP D 726 " pdb=" CB ASP D 726 " ideal model delta harmonic sigma weight residual 122.80 134.23 -11.43 0 2.50e+00 1.60e-01 2.09e+01 ... (remaining 17193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.354: 3060 0.354 - 0.708: 0 0.708 - 1.062: 0 1.062 - 1.416: 0 1.416 - 1.770: 16 Chirality restraints: 3076 Sorted by residual: chirality pdb=" CG LEU A 608 " pdb=" CB LEU A 608 " pdb=" CD1 LEU A 608 " pdb=" CD2 LEU A 608 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.83e+01 chirality pdb=" CG LEU D 608 " pdb=" CB LEU D 608 " pdb=" CD1 LEU D 608 " pdb=" CD2 LEU D 608 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.83e+01 chirality pdb=" CG LEU B 608 " pdb=" CB LEU B 608 " pdb=" CD1 LEU B 608 " pdb=" CD2 LEU B 608 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.83e+01 ... (remaining 3073 not shown) Planarity restraints: 5540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 728 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" N ARG D 729 " -0.038 2.00e-02 2.50e+03 pdb=" CA ARG D 729 " 0.009 2.00e-02 2.50e+03 pdb=" H ARG D 729 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 728 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" N ARG B 729 " -0.037 2.00e-02 2.50e+03 pdb=" CA ARG B 729 " 0.009 2.00e-02 2.50e+03 pdb=" H ARG B 729 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 728 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" N ARG C 729 " 0.037 2.00e-02 2.50e+03 pdb=" CA ARG C 729 " -0.009 2.00e-02 2.50e+03 pdb=" H ARG C 729 " -0.017 2.00e-02 2.50e+03 ... (remaining 5537 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.69: 28 1.69 - 2.42: 15668 2.42 - 3.15: 105609 3.15 - 3.87: 136269 3.87 - 4.60: 220731 Warning: very small nonbonded interaction distances. Nonbonded interactions: 478305 Sorted by model distance: nonbonded pdb=" OE2 GLU D 144 " pdb=" HE1 PHE D 193 " model vdw 0.967 2.450 nonbonded pdb=" OE2 GLU B 144 " pdb=" HE1 PHE B 193 " model vdw 0.967 2.450 nonbonded pdb=" OE2 GLU C 144 " pdb=" HE1 PHE C 193 " model vdw 0.967 2.450 nonbonded pdb=" OE2 GLU A 144 " pdb=" HE1 PHE A 193 " model vdw 0.967 2.450 nonbonded pdb="HD11 LEU D 162 " pdb=" HG CYS D 171 " model vdw 1.533 2.440 ... (remaining 478300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.010 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: 0.540 Extract box with map and model: 6.650 Check model and map are aligned: 0.550 Set scattering table: 0.290 Process input model: 106.210 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 0.056 18748 Z= 0.397 Angle : 0.855 18.524 25548 Z= 0.484 Chirality : 0.127 1.770 3076 Planarity : 0.004 0.037 3152 Dihedral : 7.647 40.125 6252 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.17 % 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: -1.96 (0.15), residues: 2428 helix: -0.77 (0.11), residues: 1544 sheet: -2.31 (0.47), residues: 68 loop : -2.05 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 710 HIS 0.007 0.001 HIS B 426 PHE 0.028 0.002 PHE C 449 TYR 0.012 0.002 TYR C 575 ARG 0.010 0.001 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.484 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 outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.7236 time to fit residues: 479.3058 Evaluate side-chains 267 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 256 HIS B 330 ASN B 645 GLN C 178 ASN C 256 HIS C 330 ASN C 645 GLN C 750 ASN A 178 ASN A 256 HIS A 330 ASN A 645 GLN A 750 ASN D 178 ASN D 256 HIS D 330 ASN D 645 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18748 Z= 0.187 Angle : 0.645 14.625 25548 Z= 0.321 Chirality : 0.123 1.715 3076 Planarity : 0.004 0.037 3152 Dihedral : 4.013 18.528 2620 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.47 % Allowed : 6.38 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2428 helix: 0.87 (0.12), residues: 1564 sheet: -1.66 (0.45), residues: 92 loop : -1.52 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 710 HIS 0.006 0.001 HIS A 256 PHE 0.015 0.001 PHE B 377 TYR 0.011 0.001 TYR A 564 ARG 0.003 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 272 time to evaluate : 2.629 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 outliers start: 8 outliers final: 8 residues processed: 276 average time/residue: 0.6223 time to fit residues: 262.3287 Evaluate side-chains 255 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 178 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18748 Z= 0.183 Angle : 0.608 15.066 25548 Z= 0.302 Chirality : 0.122 1.711 3076 Planarity : 0.003 0.028 3152 Dihedral : 3.650 16.559 2620 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.88 % Allowed : 7.49 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2428 helix: 1.67 (0.13), residues: 1576 sheet: -1.45 (0.55), residues: 68 loop : -1.38 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 493 HIS 0.003 0.000 HIS B 426 PHE 0.013 0.001 PHE B 542 TYR 0.011 0.001 TYR D 208 ARG 0.003 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 2.861 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: B 435 LYS cc_start: 0.8262 (mmtm) cc_final: 0.8028 (mmtp) REVERT: C 435 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7991 (mmtp) REVERT: C 689 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 435 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7986 (mmtp) REVERT: D 435 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7982 (mmtp) REVERT: D 689 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6848 (mt-10) outliers start: 15 outliers final: 11 residues processed: 265 average time/residue: 0.6225 time to fit residues: 252.1298 Evaluate side-chains 240 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18748 Z= 0.341 Angle : 0.673 14.781 25548 Z= 0.346 Chirality : 0.123 1.725 3076 Planarity : 0.004 0.031 3152 Dihedral : 3.988 19.973 2620 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.94 % Allowed : 7.96 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2428 helix: 1.54 (0.13), residues: 1632 sheet: -1.24 (0.57), residues: 68 loop : -1.61 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 493 HIS 0.002 0.001 HIS C 426 PHE 0.015 0.002 PHE A 259 TYR 0.022 0.002 TYR C 208 ARG 0.005 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 265 time to evaluate : 2.910 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: B 163 THR cc_start: 0.8735 (m) cc_final: 0.8492 (p) REVERT: B 555 MET cc_start: 0.8608 (tmm) cc_final: 0.8367 (tmm) REVERT: C 163 THR cc_start: 0.8748 (m) cc_final: 0.8513 (p) REVERT: C 555 MET cc_start: 0.8602 (tmm) cc_final: 0.8360 (tmm) REVERT: A 163 THR cc_start: 0.8751 (m) cc_final: 0.8514 (p) REVERT: A 555 MET cc_start: 0.8605 (tmm) cc_final: 0.8364 (tmm) REVERT: D 163 THR cc_start: 0.8755 (m) cc_final: 0.8515 (p) REVERT: D 493 TRP cc_start: 0.7523 (t-100) cc_final: 0.7290 (t-100) REVERT: D 555 MET cc_start: 0.8602 (tmm) cc_final: 0.8362 (tmm) outliers start: 16 outliers final: 12 residues processed: 273 average time/residue: 0.6735 time to fit residues: 274.1349 Evaluate side-chains 243 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0020 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18748 Z= 0.159 Angle : 0.600 14.998 25548 Z= 0.296 Chirality : 0.122 1.697 3076 Planarity : 0.002 0.020 3152 Dihedral : 3.601 18.492 2620 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.64 % Allowed : 8.37 % Favored : 89.99 % 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: 1.34 (0.17), residues: 2428 helix: 1.97 (0.13), residues: 1632 sheet: -1.24 (0.58), residues: 68 loop : -1.45 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 521 HIS 0.002 0.000 HIS D 301 PHE 0.014 0.001 PHE C 633 TYR 0.010 0.001 TYR B 564 ARG 0.003 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 268 time to evaluate : 2.673 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: B 163 THR cc_start: 0.8616 (m) cc_final: 0.8386 (p) REVERT: C 163 THR cc_start: 0.8596 (m) cc_final: 0.8369 (p) REVERT: C 493 TRP cc_start: 0.7553 (t-100) cc_final: 0.7353 (t-100) REVERT: A 163 THR cc_start: 0.8590 (m) cc_final: 0.8368 (p) REVERT: D 163 THR cc_start: 0.8598 (m) cc_final: 0.8375 (p) REVERT: D 639 LEU cc_start: 0.8575 (mp) cc_final: 0.8368 (mp) outliers start: 28 outliers final: 20 residues processed: 276 average time/residue: 0.6308 time to fit residues: 266.7914 Evaluate side-chains 274 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 254 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 671 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 18748 Z= 0.327 Angle : 0.644 14.763 25548 Z= 0.326 Chirality : 0.122 1.691 3076 Planarity : 0.003 0.021 3152 Dihedral : 3.788 20.289 2620 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.87 % Allowed : 8.78 % Favored : 89.34 % 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: 1.22 (0.17), residues: 2428 helix: 1.85 (0.13), residues: 1632 sheet: -1.27 (0.57), residues: 68 loop : -1.44 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 493 HIS 0.002 0.000 HIS B 426 PHE 0.016 0.001 PHE B 442 TYR 0.019 0.002 TYR A 208 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 2.978 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 outliers start: 32 outliers final: 21 residues processed: 271 average time/residue: 0.6166 time to fit residues: 262.0845 Evaluate side-chains 266 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18748 Z= 0.273 Angle : 0.627 14.877 25548 Z= 0.314 Chirality : 0.121 1.685 3076 Planarity : 0.003 0.021 3152 Dihedral : 3.745 20.297 2620 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.70 % Allowed : 9.66 % Favored : 88.64 % 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: 1.37 (0.17), residues: 2428 helix: 1.95 (0.13), residues: 1632 sheet: -1.33 (0.58), residues: 68 loop : -1.33 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 493 HIS 0.002 0.000 HIS B 426 PHE 0.018 0.001 PHE C 442 TYR 0.016 0.001 TYR C 208 ARG 0.004 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 2.668 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: B 493 TRP cc_start: 0.7472 (t-100) cc_final: 0.7206 (t-100) REVERT: C 493 TRP cc_start: 0.7468 (t-100) cc_final: 0.7215 (t-100) REVERT: C 548 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7491 (tt) REVERT: D 548 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7499 (tt) outliers start: 29 outliers final: 17 residues processed: 261 average time/residue: 0.5989 time to fit residues: 242.6432 Evaluate side-chains 268 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18748 Z= 0.232 Angle : 0.614 14.905 25548 Z= 0.306 Chirality : 0.121 1.687 3076 Planarity : 0.002 0.021 3152 Dihedral : 3.621 19.715 2620 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.17 % Allowed : 10.60 % Favored : 88.23 % 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: 1.54 (0.17), residues: 2428 helix: 2.09 (0.13), residues: 1632 sheet: -1.35 (0.57), residues: 68 loop : -1.28 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 493 HIS 0.002 0.001 HIS B 301 PHE 0.011 0.001 PHE A 633 TYR 0.013 0.001 TYR B 208 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 2.871 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: B 493 TRP cc_start: 0.7483 (t-100) cc_final: 0.7210 (t-100) REVERT: C 493 TRP cc_start: 0.7457 (t-100) cc_final: 0.7195 (t-100) outliers start: 20 outliers final: 16 residues processed: 253 average time/residue: 0.6168 time to fit residues: 242.4510 Evaluate side-chains 261 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.0970 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 172 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18748 Z= 0.167 Angle : 0.594 14.983 25548 Z= 0.292 Chirality : 0.121 1.692 3076 Planarity : 0.002 0.020 3152 Dihedral : 3.405 17.935 2620 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.00 % Allowed : 10.89 % Favored : 88.11 % 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: 1.85 (0.18), residues: 2428 helix: 2.36 (0.13), residues: 1632 sheet: -1.44 (0.56), residues: 68 loop : -1.23 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 493 HIS 0.002 0.000 HIS B 301 PHE 0.011 0.001 PHE A 633 TYR 0.010 0.001 TYR B 564 ARG 0.003 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 2.751 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: B 493 TRP cc_start: 0.7522 (t-100) cc_final: 0.7246 (t-100) REVERT: C 493 TRP cc_start: 0.7522 (t-100) cc_final: 0.7256 (t-100) REVERT: A 694 LEU cc_start: 0.8995 (mp) cc_final: 0.8793 (mp) outliers start: 17 outliers final: 15 residues processed: 266 average time/residue: 0.6032 time to fit residues: 247.9710 Evaluate side-chains 267 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 chunk 118 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18748 Z= 0.250 Angle : 0.616 14.861 25548 Z= 0.308 Chirality : 0.121 1.694 3076 Planarity : 0.002 0.021 3152 Dihedral : 3.538 18.801 2620 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.94 % Allowed : 11.07 % Favored : 88.00 % 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: 1.75 (0.17), residues: 2428 helix: 2.28 (0.13), residues: 1632 sheet: -1.40 (0.56), residues: 68 loop : -1.27 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 493 HIS 0.002 0.000 HIS D 426 PHE 0.010 0.001 PHE A 633 TYR 0.014 0.001 TYR B 208 ARG 0.004 0.000 ARG A 693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 620 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 2.643 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: B 493 TRP cc_start: 0.7526 (t-100) cc_final: 0.7242 (t-100) REVERT: C 493 TRP cc_start: 0.7527 (t-100) cc_final: 0.7252 (t-100) outliers start: 16 outliers final: 13 residues processed: 254 average time/residue: 0.6300 time to fit residues: 248.5363 Evaluate side-chains 258 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100481 restraints weight = 76932.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104044 restraints weight = 35280.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104536 restraints weight = 24961.419| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18748 Z= 0.172 Angle : 0.597 14.969 25548 Z= 0.294 Chirality : 0.121 1.691 3076 Planarity : 0.002 0.021 3152 Dihedral : 3.382 17.634 2620 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.05 % Allowed : 11.12 % Favored : 87.82 % 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: 2.01 (0.18), residues: 2428 helix: 2.51 (0.13), residues: 1632 sheet: -1.40 (0.56), residues: 68 loop : -1.22 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 493 HIS 0.002 0.000 HIS B 301 PHE 0.010 0.001 PHE A 633 TYR 0.010 0.001 TYR B 564 ARG 0.002 0.000 ARG B 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6481.60 seconds wall clock time: 115 minutes 2.93 seconds (6902.93 seconds total)