Starting phenix.real_space_refine on Tue Feb 20 18:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d05_7785/02_2024/6d05_7785_updated.pdb" } resolution = 3.8 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= 0.002 sd= 0.014 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.97, per 1000 atoms: 0.49 Number of scatterers: 28748 At special positions: 0 Unit cell: (171.45, 148.5, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.02 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.04 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.02 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.02 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.04 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 10.43 Conformation dependent library (CDL) restraints added in 4.7 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 20 sheets defined 46.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.802A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.676A pdb=" N ASN A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 420 through 440 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 500 through 511 removed outlier: 4.986A pdb=" N THR A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.697A pdb=" N VAL A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 634 removed outlier: 3.547A pdb=" N GLN A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.520A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.846A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 749 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.801A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.676A pdb=" N ASN B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 420 through 440 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 474 No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 500 through 511 removed outlier: 4.986A pdb=" N THR B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.697A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 634 removed outlier: 3.546A pdb=" N GLN B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 629 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 631 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 632 " --> pdb=" O TYR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.520A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 721 removed outlier: 3.846A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 749 Processing helix chain 'C' and resid 13 through 29 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.847A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 removed outlier: 3.775A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 527 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 549 through 552 No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.906A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 669 through 676 Processing helix chain 'D' and resid 13 through 29 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 188 through 196 Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 318 through 328 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.848A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.775A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 549 through 552 No H-bonds generated for 'chain 'D' and resid 549 through 552' Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.906A pdb=" N HIS D 606 " --> pdb=" O ARG D 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 669 through 676 Processing helix chain 'E' and resid 197 through 209 Processing helix chain 'E' and resid 216 through 255 removed outlier: 4.653A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 267 through 307 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 338 through 364 removed outlier: 3.931A pdb=" N LYS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 405 Processing helix chain 'E' and resid 416 through 476 removed outlier: 4.174A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 513 removed outlier: 3.590A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 512 " --> pdb=" O GLU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 567 removed outlier: 3.936A pdb=" N ASN E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 632 removed outlier: 4.931A pdb=" N PHE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 209 Processing helix chain 'F' and resid 216 through 255 removed outlier: 4.653A pdb=" N THR F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 250 " --> pdb=" O THR F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 267 through 307 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 338 through 364 removed outlier: 3.930A pdb=" N LYS F 363 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 405 Processing helix chain 'F' and resid 416 through 476 removed outlier: 4.174A pdb=" N ASP F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 513 removed outlier: 3.591A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU F 512 " --> pdb=" O GLU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 567 removed outlier: 3.936A pdb=" N ASN F 566 " --> pdb=" O SER F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 632 removed outlier: 4.929A pdb=" N PHE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER F 593 " --> pdb=" O TYR F 589 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL A 403 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 404 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A 481 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY A 406 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN A 483 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 226 through 230 removed outlier: 3.768A pdb=" N VAL A 200 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 214 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 202 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU A 212 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.601A pdb=" N ILE A 254 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 278 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 257 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 280 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A 281 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 335 " --> pdb=" O ILE A 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL B 403 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL B 404 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR B 481 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 406 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN B 483 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 226 through 230 removed outlier: 3.769A pdb=" N VAL B 200 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 214 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.601A pdb=" N ILE B 254 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 278 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 257 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 280 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE B 281 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 335 " --> pdb=" O ILE B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 8 through 10 Processing sheet with id= H, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.530A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 244 through 246 removed outlier: 4.009A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= K, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= L, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.912A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 8 through 10 Processing sheet with id= O, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.531A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 244 through 246 removed outlier: 4.008A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= R, first strand: chain 'D' and resid 342 through 347 Processing sheet with id= S, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 580 through 582 removed outlier: 3.914A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) 1322 hydrogen bonds defined for protein. 3852 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: 9.07 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9261 1.34 - 1.47: 7200 1.47 - 1.59: 12707 1.59 - 1.72: 0 1.72 - 1.84: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 96.63 - 104.16: 356 104.16 - 111.70: 13087 111.70 - 119.23: 10883 119.23 - 126.76: 14968 126.76 - 134.29: 370 Bond angle restraints: 39664 Sorted by residual: angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.62 -3.38 6.30e-01 2.52e+00 2.87e+01 angle pdb=" C LEU D 629 " pdb=" N LEU D 630 " pdb=" CA LEU D 630 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C LEU C 629 " pdb=" N LEU C 630 " pdb=" CA LEU C 630 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C ASN D 461 " pdb=" N ILE D 462 " pdb=" CA ILE D 462 " ideal model delta sigma weight residual 120.24 123.60 -3.36 6.30e-01 2.52e+00 2.85e+01 angle pdb=" C ALA C 54 " pdb=" N ASN C 55 " pdb=" CA ASN C 55 " ideal model delta sigma weight residual 122.61 130.74 -8.13 1.56e+00 4.11e-01 2.72e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 17106 22.62 - 45.23: 750 45.23 - 67.85: 101 67.85 - 90.46: 58 90.46 - 113.08: 27 Dihedral angle restraints: 18042 sinusoidal: 7570 harmonic: 10472 Sorted by residual: dihedral pdb=" CA VAL C 1 " pdb=" C VAL C 1 " pdb=" N PRO C 2 " pdb=" CA PRO C 2 " ideal model delta harmonic sigma weight residual -180.00 -93.65 -86.35 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA VAL D 1 " pdb=" C VAL D 1 " pdb=" N PRO D 2 " pdb=" CA PRO D 2 " ideal model delta harmonic sigma weight residual -180.00 -93.74 -86.26 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -105.57 -74.43 0 5.00e+00 4.00e-02 2.22e+02 ... (remaining 18039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4308 0.180 - 0.359: 42 0.359 - 0.539: 2 0.539 - 0.719: 1 0.719 - 0.899: 1 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG D 707 " pdb=" ND2 ASN D 611 " pdb=" C2 NAG D 707 " pdb=" O5 NAG D 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C 707 " pdb=" ND2 ASN C 611 " pdb=" C2 NAG C 707 " pdb=" O5 NAG C 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C GLU B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 728 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 729 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 728 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C GLU A 728 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 728 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 729 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 727 " 0.028 2.00e-02 2.50e+03 2.62e-02 8.59e+00 pdb=" CG ASN B 727 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 727 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 727 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.031 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 272 2.62 - 3.19: 24842 3.19 - 3.76: 44431 3.76 - 4.33: 59443 4.33 - 4.90: 97039 Nonbonded interactions: 226027 Sorted by model distance: nonbonded pdb=" OH TYR D 95 " pdb="FE FE D 703 " model vdw 2.046 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.051 2.260 nonbonded pdb=" OH TYR D 517 " pdb="FE FE D 701 " model vdw 2.055 2.260 nonbonded pdb=" OH TYR C 517 " pdb="FE FE C 701 " model vdw 2.066 2.260 nonbonded pdb="FE FE D 703 " pdb=" O2 CO3 D 704 " model vdw 2.078 2.260 ... (remaining 226022 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.970 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 72.290 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.091 29360 Z= 0.581 Angle : 1.137 12.840 39664 Z= 0.638 Chirality : 0.061 0.899 4354 Planarity : 0.007 0.067 5106 Dihedral : 13.781 113.078 11164 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 7.61 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 1.56 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.11), residues: 3560 helix: -1.98 (0.10), residues: 1720 sheet: -2.10 (0.23), residues: 372 loop : -2.28 (0.13), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP D 358 HIS 0.019 0.003 HIS D 249 PHE 0.039 0.004 PHE A 346 TYR 0.031 0.003 TYR F 552 ARG 0.014 0.002 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 397 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 365 MET cc_start: 0.8887 (mmm) cc_final: 0.8678 (mmm) REVERT: A 536 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 671 MET cc_start: 0.8239 (mmm) cc_final: 0.8017 (mmt) REVERT: B 246 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8205 (tm) REVERT: B 349 MET cc_start: 0.8658 (mmt) cc_final: 0.8350 (mmt) REVERT: B 453 TRP cc_start: 0.7613 (m-10) cc_final: 0.7310 (m-10) REVERT: B 655 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7547 (tpp80) REVERT: B 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7235 (m-30) REVERT: B 671 MET cc_start: 0.8791 (mmm) cc_final: 0.8217 (mmt) REVERT: C 26 MET cc_start: 0.8084 (mmt) cc_final: 0.7740 (tpp) REVERT: C 391 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9025 (pt) REVERT: C 464 MET cc_start: 0.8992 (mmt) cc_final: 0.8681 (mmm) REVERT: D 26 MET cc_start: 0.8084 (mmt) cc_final: 0.7849 (mmt) REVERT: D 464 MET cc_start: 0.8743 (mmt) cc_final: 0.8477 (mmm) REVERT: E 175 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7864 (mp) REVERT: E 306 LEU cc_start: 0.6491 (tt) cc_final: 0.6201 (tp) REVERT: F 306 LEU cc_start: 0.6458 (tt) cc_final: 0.6149 (tp) REVERT: F 324 MET cc_start: 0.6831 (tpp) cc_final: 0.5844 (mmp) REVERT: F 335 MET cc_start: 0.7409 (tmm) cc_final: 0.7109 (tmm) outliers start: 40 outliers final: 5 residues processed: 432 average time/residue: 0.4659 time to fit residues: 303.1812 Evaluate side-chains 165 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 277 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 150 ASN A 186 HIS A 275 ASN A 379 ASN A 401 HIS A 483 ASN A 615 ASN A 626 ASN A 662 ASN A 715 ASN A 722 ASN A 743 GLN B 148 ASN B 150 ASN B 186 HIS B 275 ASN B 379 ASN B 401 HIS B 483 ASN B 626 ASN B 640 GLN B 715 ASN B 722 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN C 111 GLN C 207 HIS C 213 ASN C 273 HIS C 300 HIS C 417 ASN C 443 ASN C 451 HIS C 461 ASN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN D 111 GLN D 207 HIS D 213 ASN D 268 ASN D 271 GLN D 273 HIS ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN D 451 HIS D 461 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS E 252 ASN E 263 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN E 413 GLN E 428 ASN E 444 ASN E 449 HIS E 456 ASN E 488 GLN E 503 ASN E 528 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 ASN F 212 HIS F 252 ASN F 263 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN F 372 ASN F 428 ASN F 444 ASN F 449 HIS F 456 ASN F 464 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 ASN ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 29360 Z= 0.429 Angle : 0.791 11.936 39664 Z= 0.416 Chirality : 0.048 0.355 4354 Planarity : 0.006 0.062 5106 Dihedral : 10.119 114.723 4226 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 3.90 % Allowed : 9.94 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.38 (0.13), residues: 3560 helix: 0.14 (0.12), residues: 1734 sheet: -1.74 (0.24), residues: 370 loop : -1.95 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 740 HIS 0.016 0.002 HIS F 222 PHE 0.022 0.002 PHE B 442 TYR 0.043 0.002 TYR F 525 ARG 0.010 0.001 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 161 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 246 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8542 (tm) REVERT: A 349 MET cc_start: 0.8519 (mmm) cc_final: 0.7762 (mmt) REVERT: A 365 MET cc_start: 0.8912 (mmm) cc_final: 0.8699 (mmm) REVERT: B 203 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 246 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8323 (tm) REVERT: B 671 MET cc_start: 0.8991 (mmm) cc_final: 0.8239 (mmt) REVERT: B 714 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 756 ILE cc_start: 0.8956 (mm) cc_final: 0.8599 (tt) REVERT: C 225 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8083 (pp) REVERT: C 374 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9146 (m) REVERT: C 382 MET cc_start: 0.8923 (mtp) cc_final: 0.8680 (ttm) REVERT: C 391 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8236 (pp) REVERT: D 225 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8183 (pp) REVERT: D 276 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7612 (mmmt) REVERT: D 374 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9265 (m) REVERT: D 382 MET cc_start: 0.8996 (mtp) cc_final: 0.8758 (ttm) REVERT: E 175 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7875 (mp) REVERT: F 324 MET cc_start: 0.6747 (tpp) cc_final: 0.6285 (mmp) REVERT: F 335 MET cc_start: 0.7157 (tmm) cc_final: 0.6936 (tmm) REVERT: F 357 MET cc_start: 0.6788 (ptp) cc_final: 0.6381 (ptp) REVERT: F 632 LEU cc_start: 0.3611 (OUTLIER) cc_final: 0.3154 (tt) outliers start: 122 outliers final: 62 residues processed: 268 average time/residue: 0.3619 time to fit residues: 163.7134 Evaluate side-chains 192 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 119 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 524 ASP Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 267 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 347 optimal weight: 5.9990 chunk 286 optimal weight: 0.0030 chunk 319 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 186 HIS A 401 HIS A 662 ASN B 186 HIS B 615 ASN B 684 HIS B 747 ASN C 55 ASN C 541 ASN C 546 ASN D 55 ASN D 268 ASN D 271 GLN D 300 HIS D 541 ASN D 546 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN F 528 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29360 Z= 0.186 Angle : 0.613 9.753 39664 Z= 0.317 Chirality : 0.042 0.347 4354 Planarity : 0.004 0.055 5106 Dihedral : 8.718 109.629 4226 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.97 % Allowed : 11.89 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3560 helix: 0.97 (0.12), residues: 1702 sheet: -1.50 (0.26), residues: 362 loop : -1.65 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.012 0.001 HIS F 628 PHE 0.020 0.001 PHE E 462 TYR 0.021 0.001 TYR F 525 ARG 0.004 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 142 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8683 (tm) REVERT: A 349 MET cc_start: 0.8490 (mmm) cc_final: 0.7771 (mmt) REVERT: A 374 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8042 (ptmm) REVERT: A 656 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8417 (tt) REVERT: B 246 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8450 (tm) REVERT: B 374 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8075 (ptmm) REVERT: B 671 MET cc_start: 0.8981 (mmm) cc_final: 0.8112 (mmt) REVERT: B 714 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 205 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7817 (p) REVERT: C 276 LYS cc_start: 0.7806 (mmtt) cc_final: 0.6918 (mmmt) REVERT: C 333 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6595 (pm20) REVERT: C 382 MET cc_start: 0.8789 (mtp) cc_final: 0.8584 (ttm) REVERT: D 205 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7803 (p) REVERT: D 382 MET cc_start: 0.8936 (mtp) cc_final: 0.8707 (ttm) REVERT: E 175 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7896 (mp) REVERT: E 335 MET cc_start: 0.6622 (tmm) cc_final: 0.6281 (tpp) REVERT: F 335 MET cc_start: 0.6982 (tmm) cc_final: 0.6630 (tmm) REVERT: F 632 LEU cc_start: 0.3314 (OUTLIER) cc_final: 0.2907 (tt) outliers start: 93 outliers final: 49 residues processed: 224 average time/residue: 0.3639 time to fit residues: 137.4355 Evaluate side-chains 175 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 117 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 524 ASP Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 323 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 662 ASN C 55 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN D 55 ASN D 268 ASN D 271 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 ASN E 488 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 574 GLN ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 29360 Z= 0.406 Angle : 0.702 9.599 39664 Z= 0.364 Chirality : 0.046 0.344 4354 Planarity : 0.004 0.061 5106 Dihedral : 8.102 111.248 4223 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.73 % Allowed : 11.48 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3560 helix: 1.18 (0.13), residues: 1714 sheet: -1.37 (0.26), residues: 360 loop : -1.62 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 740 HIS 0.013 0.001 HIS F 628 PHE 0.024 0.002 PHE E 462 TYR 0.028 0.002 TYR F 525 ARG 0.005 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 121 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 246 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8581 (tm) REVERT: A 349 MET cc_start: 0.8421 (mmm) cc_final: 0.7916 (mmt) REVERT: A 374 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8132 (ptmm) REVERT: A 474 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 476 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8993 (tt) REVERT: B 239 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8593 (p) REVERT: B 246 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8545 (tm) REVERT: B 374 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8100 (ptmm) REVERT: B 476 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9096 (tt) REVERT: B 671 MET cc_start: 0.9153 (mmm) cc_final: 0.8374 (mmt) REVERT: B 714 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 205 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7856 (p) REVERT: C 225 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 226 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 276 LYS cc_start: 0.7649 (mmtt) cc_final: 0.6921 (mmmt) REVERT: C 382 MET cc_start: 0.9019 (mtp) cc_final: 0.8787 (ttm) REVERT: D 26 MET cc_start: 0.8281 (mmt) cc_final: 0.8059 (mmt) REVERT: D 205 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7849 (p) REVERT: D 225 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8262 (pp) REVERT: D 226 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8886 (pp) REVERT: D 276 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7390 (mmmt) REVERT: E 175 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8020 (mp) REVERT: E 335 MET cc_start: 0.6702 (tmm) cc_final: 0.6295 (tpp) REVERT: F 335 MET cc_start: 0.7106 (tmm) cc_final: 0.6806 (tmm) outliers start: 148 outliers final: 89 residues processed: 259 average time/residue: 0.3702 time to fit residues: 160.9156 Evaluate side-chains 216 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 111 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 524 ASP Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 174 optimal weight: 0.2980 chunk 307 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 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 743 GLN C 108 GLN D 55 ASN D 268 ASN D 271 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29360 Z= 0.172 Angle : 0.599 14.371 39664 Z= 0.303 Chirality : 0.042 0.330 4354 Planarity : 0.004 0.055 5106 Dihedral : 7.544 108.221 4223 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.55 % Allowed : 13.04 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.02 (0.14), residues: 3560 helix: 1.47 (0.12), residues: 1714 sheet: -1.24 (0.27), residues: 364 loop : -1.41 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 740 HIS 0.011 0.001 HIS F 628 PHE 0.021 0.001 PHE E 462 TYR 0.043 0.001 TYR E 625 ARG 0.006 0.000 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 127 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 374 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8117 (ptmm) REVERT: B 246 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8538 (tm) REVERT: B 374 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7996 (ptmm) REVERT: B 476 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 671 MET cc_start: 0.9040 (mmm) cc_final: 0.8313 (mmt) REVERT: B 714 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 205 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7769 (p) REVERT: C 225 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8087 (pp) REVERT: C 276 LYS cc_start: 0.7630 (mmtt) cc_final: 0.6989 (mmmt) REVERT: D 4 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6684 (pttt) REVERT: D 205 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7751 (p) REVERT: D 225 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8157 (pp) REVERT: D 276 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7557 (mmmt) REVERT: D 278 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6694 (ptmm) REVERT: E 175 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7872 (mp) REVERT: E 218 TYR cc_start: 0.7840 (m-10) cc_final: 0.7519 (m-10) REVERT: E 335 MET cc_start: 0.6504 (tmm) cc_final: 0.6082 (tpp) REVERT: F 317 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6167 (mm-40) REVERT: F 335 MET cc_start: 0.6975 (tmm) cc_final: 0.6720 (tpp) REVERT: F 632 LEU cc_start: 0.3713 (OUTLIER) cc_final: 0.3499 (tt) outliers start: 111 outliers final: 72 residues processed: 226 average time/residue: 0.3440 time to fit residues: 132.2220 Evaluate side-chains 198 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 112 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 67 optimal weight: 0.0870 chunk 200 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN C 55 ASN D 108 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29360 Z= 0.270 Angle : 0.622 11.085 39664 Z= 0.317 Chirality : 0.043 0.326 4354 Planarity : 0.004 0.052 5106 Dihedral : 7.394 107.962 4223 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 4.35 % Allowed : 13.33 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.14), residues: 3560 helix: 1.55 (0.12), residues: 1732 sheet: -1.19 (0.27), residues: 360 loop : -1.41 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 740 HIS 0.013 0.001 HIS F 628 PHE 0.022 0.001 PHE E 462 TYR 0.037 0.001 TYR E 625 ARG 0.006 0.000 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 120 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 374 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8013 (ptmm) REVERT: B 239 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 246 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8587 (tm) REVERT: B 374 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8003 (ptmm) REVERT: B 476 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9051 (tt) REVERT: B 634 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: B 671 MET cc_start: 0.9087 (mmm) cc_final: 0.8367 (mmt) REVERT: B 679 MET cc_start: 0.9052 (mtt) cc_final: 0.8800 (mtm) REVERT: B 714 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 205 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7769 (p) REVERT: C 225 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8101 (pp) REVERT: C 226 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8925 (pp) REVERT: C 276 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7409 (mmmt) REVERT: C 464 MET cc_start: 0.8609 (mmm) cc_final: 0.7167 (mmm) REVERT: D 205 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7794 (p) REVERT: D 225 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8205 (pp) REVERT: D 226 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8882 (pp) REVERT: D 276 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7570 (mmmt) REVERT: D 464 MET cc_start: 0.8548 (mmm) cc_final: 0.7111 (mmm) REVERT: E 175 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7977 (mp) REVERT: E 218 TYR cc_start: 0.8115 (m-10) cc_final: 0.7904 (m-80) REVERT: F 632 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3500 (tt) outliers start: 136 outliers final: 95 residues processed: 243 average time/residue: 0.3487 time to fit residues: 144.5915 Evaluate side-chains 223 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 113 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 524 ASP Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29360 Z= 0.289 Angle : 0.625 9.484 39664 Z= 0.320 Chirality : 0.043 0.322 4354 Planarity : 0.004 0.050 5106 Dihedral : 7.254 108.058 4223 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.70 % Allowed : 13.49 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3560 helix: 1.63 (0.13), residues: 1718 sheet: -1.18 (0.27), residues: 360 loop : -1.44 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 740 HIS 0.011 0.001 HIS F 628 PHE 0.022 0.001 PHE E 462 TYR 0.047 0.002 TYR E 625 ARG 0.006 0.000 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 115 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 349 MET cc_start: 0.8892 (mmt) cc_final: 0.8209 (mmm) REVERT: A 374 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8035 (ptmm) REVERT: A 474 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B 239 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8553 (p) REVERT: B 246 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8553 (tm) REVERT: B 374 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8016 (ptmm) REVERT: B 476 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9093 (tt) REVERT: B 634 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: B 635 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8178 (ttm) REVERT: B 671 MET cc_start: 0.9152 (mmm) cc_final: 0.8429 (mmt) REVERT: B 679 MET cc_start: 0.9016 (mtt) cc_final: 0.8769 (mtm) REVERT: B 714 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7483 (tp30) REVERT: C 205 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7738 (p) REVERT: C 225 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8190 (pp) REVERT: C 226 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (pp) REVERT: C 276 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7567 (mmmt) REVERT: C 464 MET cc_start: 0.8574 (mmm) cc_final: 0.7182 (mmm) REVERT: D 205 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7779 (p) REVERT: D 225 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8176 (pp) REVERT: D 226 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8900 (pp) REVERT: D 276 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7588 (mmmt) REVERT: D 278 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6691 (ptmm) REVERT: D 382 MET cc_start: 0.9123 (ttp) cc_final: 0.8879 (ttm) REVERT: D 464 MET cc_start: 0.8527 (mmm) cc_final: 0.7121 (mmm) REVERT: E 175 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7998 (mp) REVERT: E 335 MET cc_start: 0.6034 (tpt) cc_final: 0.5686 (tpp) REVERT: F 218 TYR cc_start: 0.8035 (m-10) cc_final: 0.7782 (m-80) REVERT: F 632 LEU cc_start: 0.3529 (OUTLIER) cc_final: 0.3318 (tt) outliers start: 147 outliers final: 108 residues processed: 248 average time/residue: 0.3491 time to fit residues: 147.9677 Evaluate side-chains 238 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 112 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 524 ASP Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.0270 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 0.0030 chunk 66 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 overall best weight: 1.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN B 603 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 ASN E 391 HIS ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 372 ASN F 391 HIS ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29360 Z= 0.161 Angle : 0.577 9.625 39664 Z= 0.290 Chirality : 0.041 0.308 4354 Planarity : 0.004 0.048 5106 Dihedral : 6.916 106.235 4223 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.74 % Allowed : 14.51 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3560 helix: 1.81 (0.13), residues: 1722 sheet: -1.10 (0.27), residues: 362 loop : -1.33 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 740 HIS 0.012 0.001 HIS F 628 PHE 0.020 0.001 PHE F 462 TYR 0.031 0.001 TYR E 625 ARG 0.007 0.000 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 124 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8506 (p) REVERT: A 374 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8289 (tttp) REVERT: A 474 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 634 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7823 (pp20) REVERT: B 239 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8557 (p) REVERT: B 246 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8485 (tm) REVERT: B 374 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8296 (tttp) REVERT: B 476 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9021 (tt) REVERT: B 485 ASP cc_start: 0.8140 (t0) cc_final: 0.7900 (t70) REVERT: B 634 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7816 (pp20) REVERT: B 671 MET cc_start: 0.9039 (mmm) cc_final: 0.8375 (mmt) REVERT: B 679 MET cc_start: 0.9005 (mtt) cc_final: 0.8729 (mtm) REVERT: B 684 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8507 (m-70) REVERT: B 714 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7354 (tp30) REVERT: C 205 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7653 (p) REVERT: C 225 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8151 (pp) REVERT: C 464 MET cc_start: 0.8477 (mmm) cc_final: 0.7148 (mmm) REVERT: D 225 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8179 (pp) REVERT: D 276 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7638 (mmmt) REVERT: D 278 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6671 (ptmm) REVERT: D 382 MET cc_start: 0.9069 (ttp) cc_final: 0.8866 (ttm) REVERT: E 175 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7866 (mp) REVERT: F 218 TYR cc_start: 0.7941 (m-10) cc_final: 0.7671 (m-80) outliers start: 117 outliers final: 80 residues processed: 231 average time/residue: 0.3459 time to fit residues: 138.0323 Evaluate side-chains 210 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 115 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 316 optimal weight: 0.0670 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN B 615 ASN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29360 Z= 0.216 Angle : 0.587 9.481 39664 Z= 0.297 Chirality : 0.042 0.391 4354 Planarity : 0.004 0.047 5106 Dihedral : 6.851 106.098 4223 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.58 % Allowed : 15.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % 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: 0.42 (0.14), residues: 3560 helix: 1.87 (0.13), residues: 1720 sheet: -1.07 (0.28), residues: 362 loop : -1.32 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 441 HIS 0.014 0.001 HIS B 603 PHE 0.021 0.001 PHE F 462 TYR 0.050 0.001 TYR E 625 ARG 0.008 0.000 ARG E 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 117 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 349 MET cc_start: 0.8829 (mmp) cc_final: 0.8509 (mmm) REVERT: A 474 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 634 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7851 (pp20) REVERT: B 239 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8462 (p) REVERT: B 246 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8525 (tm) REVERT: B 363 CYS cc_start: 0.6470 (t) cc_final: 0.5302 (t) REVERT: B 374 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8080 (ptmm) REVERT: B 476 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9062 (tt) REVERT: B 634 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7865 (pp20) REVERT: B 671 MET cc_start: 0.9123 (mmm) cc_final: 0.8409 (mmt) REVERT: B 679 MET cc_start: 0.9000 (mtt) cc_final: 0.8751 (mtm) REVERT: B 714 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7404 (tp30) REVERT: C 225 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8182 (pp) REVERT: C 276 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7162 (mmmt) REVERT: C 464 MET cc_start: 0.8543 (mmm) cc_final: 0.7209 (mmm) REVERT: D 225 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8220 (pp) REVERT: D 226 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8825 (pp) REVERT: D 276 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7592 (mmmt) REVERT: D 278 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6686 (ptmm) REVERT: D 382 MET cc_start: 0.9110 (ttp) cc_final: 0.8865 (ttm) REVERT: E 175 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.7950 (mp) REVERT: E 335 MET cc_start: 0.6132 (tpt) cc_final: 0.5922 (tpp) REVERT: F 218 TYR cc_start: 0.8024 (m-10) cc_final: 0.7733 (m-80) outliers start: 112 outliers final: 88 residues processed: 219 average time/residue: 0.3412 time to fit residues: 129.4390 Evaluate side-chains 213 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 112 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 159 optimal weight: 0.0670 chunk 233 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 280 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 172 optimal weight: 0.4980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29360 Z= 0.161 Angle : 0.570 9.531 39664 Z= 0.287 Chirality : 0.041 0.304 4354 Planarity : 0.004 0.048 5106 Dihedral : 6.706 105.169 4223 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.39 % Allowed : 15.15 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % 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: 0.52 (0.14), residues: 3560 helix: 1.94 (0.12), residues: 1718 sheet: -1.02 (0.28), residues: 362 loop : -1.26 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 441 HIS 0.010 0.001 HIS F 628 PHE 0.020 0.001 PHE F 462 TYR 0.032 0.001 TYR E 500 ARG 0.009 0.000 ARG E 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 119 time to evaluate : 3.378 Fit side-chains revert: symmetry clash REVERT: A 239 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 474 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8682 (pp) REVERT: A 634 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7815 (pp20) REVERT: B 239 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 246 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8502 (tm) REVERT: B 374 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (tttp) REVERT: B 476 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 485 ASP cc_start: 0.8141 (t0) cc_final: 0.7906 (t70) REVERT: B 634 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7849 (pp20) REVERT: B 671 MET cc_start: 0.9115 (mmm) cc_final: 0.8362 (mmt) REVERT: B 679 MET cc_start: 0.8990 (mtt) cc_final: 0.8733 (mtm) REVERT: B 714 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7355 (tp30) REVERT: C 26 MET cc_start: 0.7627 (mmt) cc_final: 0.7204 (mmp) REVERT: C 225 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8198 (pp) REVERT: C 276 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7079 (mmmt) REVERT: C 464 MET cc_start: 0.8482 (mmm) cc_final: 0.7259 (mmm) REVERT: D 26 MET cc_start: 0.7554 (mmt) cc_final: 0.7197 (mmp) REVERT: D 225 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8229 (pp) REVERT: D 276 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7653 (mmmt) REVERT: D 278 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6864 (ptpp) REVERT: D 382 MET cc_start: 0.9014 (ttp) cc_final: 0.8754 (ttm) REVERT: E 175 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.7920 (mp) REVERT: F 218 TYR cc_start: 0.7928 (m-10) cc_final: 0.7662 (m-80) outliers start: 106 outliers final: 82 residues processed: 216 average time/residue: 0.3413 time to fit residues: 127.8226 Evaluate side-chains 206 residues out of total 3128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 112 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 258 optimal weight: 0.3980 chunk 41 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 281 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN B 615 ASN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080096 restraints weight = 64125.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078976 restraints weight = 76911.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079812 restraints weight = 85282.697| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29360 Z= 0.163 Angle : 0.565 9.652 39664 Z= 0.284 Chirality : 0.041 0.301 4354 Planarity : 0.004 0.046 5106 Dihedral : 6.602 104.320 4223 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.26 % Allowed : 15.12 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % 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: 0.58 (0.14), residues: 3560 helix: 1.99 (0.13), residues: 1718 sheet: -0.98 (0.28), residues: 362 loop : -1.22 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 740 HIS 0.010 0.001 HIS F 628 PHE 0.020 0.001 PHE F 462 TYR 0.051 0.001 TYR E 625 ARG 0.009 0.000 ARG F 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.92 seconds wall clock time: 84 minutes 30.25 seconds (5070.25 seconds total)