Starting phenix.real_space_refine on Thu Mar 14 22:04:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y63_33632/03_2024/7y63_33632.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 66 5.16 5 C 6430 2.51 5 N 1604 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 713": "OD1" <-> "OD2" Residue "B TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 779": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" 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: "D" 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: "E" 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: "F" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9924 At special positions: 0 Unit cell: (108.692, 80.1467, 133.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 66 16.00 O 1822 8.00 N 1604 7.00 C 6430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.04 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 27 " " NAG A 903 " - " ASN A 141 " " NAG A 904 " - " ASN A 123 " " NAG B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 54 " " NAG F 1 " - " ASN B 165 " Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 479 removed outlier: 3.579A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 3.916A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.538A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 626 Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.851A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.906A pdb=" N LEU A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.556A pdb=" N CYS A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 755 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 763 " --> pdb=" O TRP A 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 813 " --> pdb=" O GLY A 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.580A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.917A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'B' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 529 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 531 " --> pdb=" O HIS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 549 through 561 removed outlier: 3.539A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 626 Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.850A pdb=" N THR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.907A pdb=" N LEU B 728 " --> pdb=" O CYS B 724 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 736 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 769 removed outlier: 3.555A pdb=" N CYS B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 763 " --> pdb=" O TRP B 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 813 " --> pdb=" O GLY B 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP A 41 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.602A pdb=" N PHE A 164 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 285 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.473A pdb=" N CYS A 197 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP B 41 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 115 Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.601A pdb=" N PHE B 164 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 285 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.472A pdb=" N CYS B 197 " --> pdb=" O LYS B 250 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1386 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: 2.86 Time building geometry restraints manager: 4.33 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: 3094 1.34 - 1.46: 2472 1.46 - 1.58: 4476 1.58 - 1.70: 0 1.70 - 1.83: 98 Bond restraints: 10140 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG A 85 " pdb=" CB ARG A 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.60e+00 ... (remaining 10135 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.75: 253 106.75 - 113.58: 5666 113.58 - 120.42: 3894 120.42 - 127.25: 3895 127.25 - 134.09: 80 Bond angle restraints: 13788 Sorted by residual: angle pdb=" C ALA A 715 " pdb=" CA ALA A 715 " pdb=" CB ALA A 715 " ideal model delta sigma weight residual 110.88 116.78 -5.90 1.57e+00 4.06e-01 1.41e+01 angle pdb=" N PHE A 195 " pdb=" CA PHE A 195 " pdb=" C PHE A 195 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.46 -7.65 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N SER A 716 " pdb=" CA SER A 716 " pdb=" C SER A 716 " ideal model delta sigma weight residual 111.75 115.84 -4.09 1.28e+00 6.10e-01 1.02e+01 angle pdb=" C ALA B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta sigma weight residual 121.80 114.40 7.40 2.44e+00 1.68e-01 9.19e+00 ... (remaining 13783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5690 23.21 - 46.42: 346 46.42 - 69.63: 69 69.63 - 92.83: 25 92.83 - 116.04: 30 Dihedral angle restraints: 6160 sinusoidal: 2526 harmonic: 3634 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 127.86 52.14 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 127.89 52.11 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual 93.00 172.68 -79.68 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 6157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1574 0.104 - 0.207: 61 0.207 - 0.311: 5 0.311 - 0.415: 2 0.415 - 0.519: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1641 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO B 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 78 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.036 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1457 2.75 - 3.29: 9676 3.29 - 3.83: 15673 3.83 - 4.36: 19202 4.36 - 4.90: 32813 Nonbonded interactions: 78821 Sorted by model distance: nonbonded pdb=" NH2 ARG A 59 " pdb=" O LYS A 122 " model vdw 2.214 2.520 nonbonded pdb=" NH2 ARG B 59 " pdb=" O LYS B 122 " model vdw 2.214 2.520 nonbonded pdb=" O THR A 224 " pdb=" NH1 ARG A 781 " model vdw 2.221 2.520 nonbonded pdb=" O THR B 224 " pdb=" NH1 ARG B 781 " model vdw 2.221 2.520 nonbonded pdb=" CD2 LEU A 81 " pdb=" CG2 VAL B 90 " model vdw 2.228 3.880 ... (remaining 78816 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 10140 Z= 0.358 Angle : 0.702 7.662 13788 Z= 0.384 Chirality : 0.053 0.519 1644 Planarity : 0.005 0.098 1718 Dihedral : 18.687 116.042 3784 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.23), residues: 1218 helix: -1.22 (0.23), residues: 468 sheet: -1.13 (0.30), residues: 296 loop : -1.79 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 700 HIS 0.003 0.001 HIS A 492 PHE 0.016 0.002 PHE A 576 TYR 0.018 0.002 TYR A 173 ARG 0.003 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.094 Fit side-chains REVERT: A 694 MET cc_start: 0.5732 (mpp) cc_final: 0.5361 (mpp) REVERT: A 728 LEU cc_start: 0.9087 (mt) cc_final: 0.8840 (mt) REVERT: A 749 LEU cc_start: 0.8529 (tp) cc_final: 0.8255 (pp) REVERT: B 694 MET cc_start: 0.5776 (mpp) cc_final: 0.5413 (mpp) REVERT: B 728 LEU cc_start: 0.9073 (mt) cc_final: 0.8828 (mt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1965 time to fit residues: 43.4485 Evaluate side-chains 132 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10140 Z= 0.324 Angle : 0.710 10.379 13788 Z= 0.356 Chirality : 0.050 0.310 1644 Planarity : 0.006 0.091 1718 Dihedral : 14.934 87.504 1620 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.14 % Allowed : 7.01 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1218 helix: -0.41 (0.22), residues: 508 sheet: -0.92 (0.30), residues: 296 loop : -1.68 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.015 0.002 PHE A 582 TYR 0.020 0.002 TYR B 584 ARG 0.004 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.936 Fit side-chains REVERT: A 297 MET cc_start: 0.6986 (ptt) cc_final: 0.6618 (ptt) REVERT: A 694 MET cc_start: 0.6092 (mpp) cc_final: 0.5803 (mpp) REVERT: A 728 LEU cc_start: 0.8906 (mt) cc_final: 0.8679 (mt) REVERT: B 104 GLN cc_start: 0.8562 (pm20) cc_final: 0.8312 (pm20) REVERT: B 297 MET cc_start: 0.6882 (ptt) cc_final: 0.6514 (ptt) REVERT: B 694 MET cc_start: 0.6023 (mpp) cc_final: 0.5758 (mpp) REVERT: B 728 LEU cc_start: 0.8909 (mt) cc_final: 0.8684 (mt) outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 0.2041 time to fit residues: 44.2700 Evaluate side-chains 137 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 215 ASN A 575 ASN ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 215 ASN B 575 ASN ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10140 Z= 0.274 Angle : 0.646 10.482 13788 Z= 0.320 Chirality : 0.047 0.275 1644 Planarity : 0.005 0.086 1718 Dihedral : 10.083 53.799 1620 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.89 % Allowed : 11.55 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1218 helix: 0.17 (0.23), residues: 514 sheet: -0.72 (0.30), residues: 296 loop : -1.71 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 634 HIS 0.002 0.001 HIS A 492 PHE 0.019 0.002 PHE B 714 TYR 0.015 0.002 TYR A 485 ARG 0.004 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.161 Fit side-chains REVERT: A 61 ARG cc_start: 0.6699 (mpt180) cc_final: 0.6493 (mtm-85) REVERT: A 94 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7550 (pp30) REVERT: A 104 GLN cc_start: 0.8495 (pm20) cc_final: 0.8212 (pm20) REVERT: A 297 MET cc_start: 0.6932 (ptt) cc_final: 0.6636 (ptt) REVERT: A 728 LEU cc_start: 0.8882 (mt) cc_final: 0.8676 (mt) REVERT: B 61 ARG cc_start: 0.6718 (mpt180) cc_final: 0.6491 (mtm-85) REVERT: B 94 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7571 (pp30) REVERT: B 104 GLN cc_start: 0.8534 (pm20) cc_final: 0.8253 (pm20) REVERT: B 297 MET cc_start: 0.6770 (ptt) cc_final: 0.6459 (ptt) REVERT: B 728 LEU cc_start: 0.8887 (mt) cc_final: 0.8676 (mt) outliers start: 20 outliers final: 10 residues processed: 153 average time/residue: 0.1971 time to fit residues: 43.9376 Evaluate side-chains 139 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10140 Z= 0.224 Angle : 0.580 7.901 13788 Z= 0.293 Chirality : 0.045 0.266 1644 Planarity : 0.004 0.082 1718 Dihedral : 8.088 53.342 1620 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.52 % Allowed : 14.30 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.81 (0.24), residues: 1218 helix: 0.49 (0.23), residues: 506 sheet: -0.68 (0.29), residues: 296 loop : -1.58 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 634 HIS 0.002 0.001 HIS A 492 PHE 0.014 0.001 PHE A 714 TYR 0.013 0.001 TYR A 173 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.061 Fit side-chains REVERT: A 94 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7521 (pp30) REVERT: A 104 GLN cc_start: 0.8473 (pm20) cc_final: 0.8218 (pm20) REVERT: A 297 MET cc_start: 0.6842 (ptt) cc_final: 0.6520 (ptt) REVERT: A 694 MET cc_start: 0.5742 (mpp) cc_final: 0.5447 (mpp) REVERT: B 94 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: B 104 GLN cc_start: 0.8531 (pm20) cc_final: 0.8262 (pm20) REVERT: B 297 MET cc_start: 0.6745 (ptt) cc_final: 0.6427 (ptt) REVERT: B 694 MET cc_start: 0.5805 (mpp) cc_final: 0.5474 (mpp) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.1825 time to fit residues: 39.9049 Evaluate side-chains 135 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 105 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10140 Z= 0.299 Angle : 0.597 7.470 13788 Z= 0.303 Chirality : 0.046 0.251 1644 Planarity : 0.005 0.084 1718 Dihedral : 7.775 54.560 1620 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.99 % Allowed : 17.05 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.78 (0.24), residues: 1218 helix: 0.52 (0.23), residues: 514 sheet: -0.61 (0.29), residues: 296 loop : -1.66 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 634 HIS 0.003 0.001 HIS A 492 PHE 0.017 0.002 PHE B 304 TYR 0.015 0.002 TYR B 173 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.104 Fit side-chains REVERT: A 94 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: A 104 GLN cc_start: 0.8494 (pm20) cc_final: 0.8254 (pm20) REVERT: A 297 MET cc_start: 0.6824 (ptt) cc_final: 0.6574 (ptt) REVERT: A 728 LEU cc_start: 0.8960 (mt) cc_final: 0.8747 (pp) REVERT: B 94 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7523 (pp30) REVERT: B 104 GLN cc_start: 0.8546 (pm20) cc_final: 0.8272 (pm20) REVERT: B 297 MET cc_start: 0.6836 (ptt) cc_final: 0.6574 (ptt) REVERT: B 728 LEU cc_start: 0.8960 (mt) cc_final: 0.8747 (pp) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.1695 time to fit residues: 36.9970 Evaluate side-chains 135 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 273 GLN A 774 GLN B 110 GLN B 774 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10140 Z= 0.181 Angle : 0.541 7.308 13788 Z= 0.276 Chirality : 0.044 0.258 1644 Planarity : 0.004 0.077 1718 Dihedral : 7.169 52.211 1620 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.37 % Allowed : 17.23 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.60 (0.24), residues: 1218 helix: 0.77 (0.23), residues: 506 sheet: -0.56 (0.29), residues: 296 loop : -1.65 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 320 HIS 0.002 0.001 HIS A 492 PHE 0.014 0.001 PHE B 304 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.149 Fit side-chains REVERT: A 94 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7540 (pp30) REVERT: A 104 GLN cc_start: 0.8470 (pm20) cc_final: 0.8230 (pm20) REVERT: A 313 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7803 (tp) REVERT: A 521 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7861 (tp) REVERT: A 694 MET cc_start: 0.5750 (mpp) cc_final: 0.5425 (mpp) REVERT: A 761 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: A 797 ASP cc_start: 0.8302 (m-30) cc_final: 0.8027 (m-30) REVERT: B 94 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: B 104 GLN cc_start: 0.8468 (pm20) cc_final: 0.8233 (pm20) REVERT: B 297 MET cc_start: 0.6707 (ptt) cc_final: 0.6490 (ptt) REVERT: B 313 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 521 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 694 MET cc_start: 0.5801 (mpp) cc_final: 0.5443 (mpp) REVERT: B 761 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: B 812 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8266 (mp) outliers start: 25 outliers final: 10 residues processed: 150 average time/residue: 0.1784 time to fit residues: 40.0201 Evaluate side-chains 146 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.0270 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10140 Z= 0.163 Angle : 0.528 7.173 13788 Z= 0.269 Chirality : 0.043 0.252 1644 Planarity : 0.004 0.079 1718 Dihedral : 6.635 52.498 1620 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.37 % Allowed : 17.90 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.43 (0.24), residues: 1218 helix: 0.98 (0.23), residues: 508 sheet: -0.46 (0.29), residues: 294 loop : -1.68 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 634 HIS 0.003 0.001 HIS B 796 PHE 0.017 0.001 PHE A 714 TYR 0.011 0.001 TYR A 173 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.046 Fit side-chains REVERT: A 94 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7406 (pp30) REVERT: A 521 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7764 (tp) REVERT: A 728 LEU cc_start: 0.8969 (mt) cc_final: 0.8725 (pp) REVERT: A 797 ASP cc_start: 0.8302 (m-30) cc_final: 0.8030 (m-30) REVERT: A 812 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 94 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7392 (pp30) REVERT: B 521 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7781 (tp) REVERT: B 694 MET cc_start: 0.5823 (mpp) cc_final: 0.5443 (mpp) outliers start: 25 outliers final: 14 residues processed: 157 average time/residue: 0.1823 time to fit residues: 42.2341 Evaluate side-chains 144 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 106 optimal weight: 30.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10140 Z= 0.216 Angle : 0.553 9.165 13788 Z= 0.282 Chirality : 0.044 0.249 1644 Planarity : 0.004 0.077 1718 Dihedral : 6.574 53.690 1620 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.12 % Allowed : 17.33 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.31 (0.24), residues: 1218 helix: 1.12 (0.23), residues: 508 sheet: -0.41 (0.29), residues: 294 loop : -1.68 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 320 HIS 0.003 0.001 HIS A 492 PHE 0.023 0.001 PHE B 304 TYR 0.013 0.001 TYR B 173 ARG 0.004 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.005 Fit side-chains REVERT: A 94 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7429 (pp30) REVERT: A 313 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 521 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7785 (tp) REVERT: A 694 MET cc_start: 0.5748 (mpp) cc_final: 0.5472 (mpp) REVERT: A 728 LEU cc_start: 0.8963 (mt) cc_final: 0.8758 (pp) REVERT: A 812 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 94 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7450 (pp30) REVERT: B 313 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7794 (tp) REVERT: B 521 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 694 MET cc_start: 0.5852 (mpp) cc_final: 0.5519 (mpp) REVERT: B 728 LEU cc_start: 0.8977 (mt) cc_final: 0.8752 (pp) REVERT: B 812 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8269 (mp) outliers start: 33 outliers final: 22 residues processed: 150 average time/residue: 0.1721 time to fit residues: 39.0382 Evaluate side-chains 153 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10140 Z= 0.244 Angle : 0.565 8.033 13788 Z= 0.288 Chirality : 0.044 0.244 1644 Planarity : 0.004 0.080 1718 Dihedral : 6.528 54.930 1620 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.75 % Allowed : 18.18 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.23 (0.24), residues: 1218 helix: 1.21 (0.23), residues: 508 sheet: -0.40 (0.29), residues: 294 loop : -1.64 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.004 0.001 HIS B 527 PHE 0.023 0.001 PHE A 304 TYR 0.014 0.001 TYR A 173 ARG 0.002 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.221 Fit side-chains REVERT: A 94 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7525 (pp30) REVERT: A 313 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 521 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7787 (tp) REVERT: A 694 MET cc_start: 0.5797 (mpp) cc_final: 0.5499 (mpp) REVERT: A 728 LEU cc_start: 0.8956 (mt) cc_final: 0.8732 (pp) REVERT: A 812 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 94 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7504 (pp30) REVERT: B 313 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 521 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 694 MET cc_start: 0.5807 (mpp) cc_final: 0.5451 (mpp) REVERT: B 728 LEU cc_start: 0.8979 (mt) cc_final: 0.8764 (pp) REVERT: B 812 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8272 (mp) outliers start: 29 outliers final: 20 residues processed: 142 average time/residue: 0.1794 time to fit residues: 38.4469 Evaluate side-chains 147 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10140 Z= 0.190 Angle : 0.546 7.238 13788 Z= 0.278 Chirality : 0.043 0.250 1644 Planarity : 0.004 0.076 1718 Dihedral : 6.282 53.809 1620 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.46 % Allowed : 18.84 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1218 helix: 1.36 (0.23), residues: 508 sheet: -0.38 (0.29), residues: 294 loop : -1.61 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 320 HIS 0.005 0.001 HIS B 527 PHE 0.028 0.001 PHE A 714 TYR 0.013 0.001 TYR B 173 ARG 0.003 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.091 Fit side-chains REVERT: A 94 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7466 (pp30) REVERT: A 104 GLN cc_start: 0.8491 (pm20) cc_final: 0.8288 (pm20) REVERT: A 313 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7772 (tp) REVERT: A 694 MET cc_start: 0.5673 (mpp) cc_final: 0.5348 (mpp) REVERT: A 728 LEU cc_start: 0.8997 (mt) cc_final: 0.8722 (pp) REVERT: A 736 MET cc_start: 0.8445 (tmm) cc_final: 0.8190 (tmm) REVERT: A 812 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 94 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: B 313 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 521 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7783 (tp) REVERT: B 694 MET cc_start: 0.5756 (mpp) cc_final: 0.5328 (mpp) REVERT: B 728 LEU cc_start: 0.8997 (mt) cc_final: 0.8735 (pp) REVERT: B 812 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8265 (mp) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.1801 time to fit residues: 38.0597 Evaluate side-chains 144 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.165949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112132 restraints weight = 13476.276| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.73 r_work: 0.3384 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10140 Z= 0.183 Angle : 0.541 6.819 13788 Z= 0.277 Chirality : 0.043 0.249 1644 Planarity : 0.004 0.078 1718 Dihedral : 6.146 53.984 1620 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.37 % Allowed : 18.84 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.01 (0.24), residues: 1218 helix: 1.43 (0.23), residues: 506 sheet: -0.36 (0.29), residues: 294 loop : -1.49 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 320 HIS 0.005 0.001 HIS B 527 PHE 0.034 0.001 PHE A 714 TYR 0.014 0.001 TYR A 729 ARG 0.002 0.000 ARG B 598 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.64 seconds wall clock time: 36 minutes 44.44 seconds (2204.44 seconds total)