Starting phenix.real_space_refine on Tue Feb 20 14:09:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teb_25844/02_2024/7teb_25844.pdb" } resolution = 4.23 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= 0.054 sd= 0.469 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 17990 2.51 5 N 4710 2.21 5 O 5287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 793": "OE1" <-> "OE2" Residue "C TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 531": "OE1" <-> "OE2" Residue "D GLU 793": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M PHE 109": "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: 28161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 751} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6177 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6186 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 752} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6177 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 14.30, per 1000 atoms: 0.51 Number of scatterers: 28161 At special positions: 0 Unit cell: (146.59, 226.05, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5287 8.00 N 4710 7.00 C 17990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=1.53 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=1.81 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.28 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.13 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=1.54 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=1.86 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.05 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=1.80 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.21 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 Time building additional restraints: 10.12 Conformation dependent library (CDL) restraints added in 4.9 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6644 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 41 sheets defined 34.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.646A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.827A pdb=" N SER A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.145A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 4.168A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.727A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 6.442A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.126A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.699A pdb=" N ARG A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.341A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.662A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 4.204A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.646A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.722A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 547' Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.750A pdb=" N PHE A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 removed outlier: 3.828A pdb=" N GLY A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.541A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 4.089A pdb=" N ASN A 689 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP A 690 " --> pdb=" O GLY A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 690' Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.550A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 removed outlier: 3.525A pdb=" N GLU A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.830A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 5.097A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 4.310A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.656A pdb=" N ILE A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.591A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.700A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.552A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.730A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.651A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 289 through 303 removed outlier: 3.647A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.184A pdb=" N MET B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.581A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.553A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.651A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 521' Processing helix chain 'B' and resid 557 through 567 removed outlier: 4.398A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.794A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.822A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 4.244A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.794A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.709A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.774A pdb=" N VAL B 776 " --> pdb=" O TRP B 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 793 through 796 Processing helix chain 'B' and resid 813 through 817 removed outlier: 4.157A pdb=" N ASP B 816 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 817' Processing helix chain 'B' and resid 818 through 838 removed outlier: 4.033A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.647A pdb=" N ASN C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.830A pdb=" N SER C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 111 removed outlier: 4.145A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 4.126A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 removed outlier: 3.728A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 6.443A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.626A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 removed outlier: 3.700A pdb=" N ARG C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.663A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 4.203A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.646A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.722A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 547' Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.750A pdb=" N PHE C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 636 removed outlier: 3.828A pdb=" N GLY C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.540A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 removed outlier: 4.089A pdb=" N ASN C 689 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 690 " --> pdb=" O GLY C 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 690' Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.550A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 removed outlier: 3.525A pdb=" N GLU C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.830A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 5.096A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 791 removed outlier: 4.311A pdb=" N GLN C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 803 removed outlier: 3.655A pdb=" N ILE C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.590A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.701A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.553A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.730A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.651A pdb=" N ASN D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.646A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 4.184A pdb=" N MET D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.582A pdb=" N LYS D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 472 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.551A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.651A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 521' Processing helix chain 'D' and resid 557 through 567 removed outlier: 4.397A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.794A pdb=" N PHE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 3.823A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 4.244A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.794A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.710A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.774A pdb=" N VAL D 776 " --> pdb=" O TRP D 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 793 through 796 Processing helix chain 'D' and resid 813 through 817 removed outlier: 4.157A pdb=" N ASP D 816 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 817 " --> pdb=" O ASP D 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 813 through 817' Processing helix chain 'D' and resid 818 through 838 removed outlier: 4.032A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.087A pdb=" N ILE A 163 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 214 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 216 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 167 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.305A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.734A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 434 Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.609A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.710A pdb=" N ARG B 67 " --> pdb=" O ILE B 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.604A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 removed outlier: 5.709A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 279 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB2, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.194A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 490 removed outlier: 4.081A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.997A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB7, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.557A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 217 removed outlier: 6.086A pdb=" N ILE C 163 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 214 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 216 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 292 removed outlier: 6.209A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.734A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.868A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.608A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.709A pdb=" N ARG D 67 " --> pdb=" O ILE D 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 97 through 100 removed outlier: 6.605A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 256 through 257 removed outlier: 5.709A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 279 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 362 through 363 Processing sheet with id=AC9, first strand: chain 'D' and resid 408 through 410 removed outlier: 6.193A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 488 through 490 removed outlier: 4.081A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.998A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'D' and resid 534 through 538 removed outlier: 3.557A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.618A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.838A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.838A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.764A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE L 21 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.643A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU M 81 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS M 22 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU M 79 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.826A pdb=" N SER M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.764A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE N 21 " --> pdb=" O PHE N 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.643A pdb=" N THR N 101 " --> pdb=" O TYR N 86 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 10.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4668 1.32 - 1.46: 11072 1.46 - 1.61: 12735 1.61 - 1.75: 2 1.75 - 1.90: 296 Bond restraints: 28773 Sorted by residual: bond pdb=" C ILE D 108 " pdb=" O ILE D 108 " ideal model delta sigma weight residual 1.232 1.272 -0.041 1.15e-02 7.56e+03 1.24e+01 bond pdb=" C ILE B 108 " pdb=" O ILE B 108 " ideal model delta sigma weight residual 1.232 1.272 -0.040 1.15e-02 7.56e+03 1.24e+01 bond pdb=" CA PHE B 176 " pdb=" CB PHE B 176 " ideal model delta sigma weight residual 1.526 1.578 -0.052 1.59e-02 3.96e+03 1.05e+01 bond pdb=" CA PHE D 176 " pdb=" CB PHE D 176 " ideal model delta sigma weight residual 1.526 1.578 -0.052 1.59e-02 3.96e+03 1.05e+01 bond pdb=" CB CYS A 457 " pdb=" SG CYS A 457 " ideal model delta sigma weight residual 1.808 1.899 -0.091 3.30e-02 9.18e+02 7.64e+00 ... (remaining 28768 not shown) Histogram of bond angle deviations from ideal: 97.56 - 105.29: 630 105.29 - 113.03: 14849 113.03 - 120.76: 13507 120.76 - 128.49: 9707 128.49 - 136.23: 261 Bond angle restraints: 38954 Sorted by residual: angle pdb=" CA CYS C 476 " pdb=" CB CYS C 476 " pdb=" SG CYS C 476 " ideal model delta sigma weight residual 114.40 136.23 -21.83 2.30e+00 1.89e-01 9.00e+01 angle pdb=" CA CYS A 476 " pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " ideal model delta sigma weight residual 114.40 136.22 -21.82 2.30e+00 1.89e-01 9.00e+01 angle pdb=" N GLY A 265 " pdb=" CA GLY A 265 " pdb=" C GLY A 265 " ideal model delta sigma weight residual 110.69 98.40 12.29 1.33e+00 5.65e-01 8.54e+01 angle pdb=" N GLY B 377 " pdb=" CA GLY B 377 " pdb=" C GLY B 377 " ideal model delta sigma weight residual 110.66 128.21 -17.55 1.90e+00 2.77e-01 8.54e+01 angle pdb=" N GLY D 377 " pdb=" CA GLY D 377 " pdb=" C GLY D 377 " ideal model delta sigma weight residual 110.66 128.21 -17.55 1.90e+00 2.77e-01 8.53e+01 ... (remaining 38949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 15711 23.27 - 46.54: 1267 46.54 - 69.81: 172 69.81 - 93.08: 37 93.08 - 116.35: 2 Dihedral angle restraints: 17189 sinusoidal: 6845 harmonic: 10344 Sorted by residual: dihedral pdb=" CA GLN D 357 " pdb=" C GLN D 357 " pdb=" N MET D 358 " pdb=" CA MET D 358 " ideal model delta harmonic sigma weight residual 180.00 63.65 116.35 0 5.00e+00 4.00e-02 5.41e+02 dihedral pdb=" CA GLN B 357 " pdb=" C GLN B 357 " pdb=" N MET B 358 " pdb=" CA MET B 358 " ideal model delta harmonic sigma weight residual 180.00 63.67 116.33 0 5.00e+00 4.00e-02 5.41e+02 dihedral pdb=" CA PRO A 403 " pdb=" C PRO A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 107.33 72.67 0 5.00e+00 4.00e-02 2.11e+02 ... (remaining 17186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3798 0.105 - 0.210: 478 0.210 - 0.315: 50 0.315 - 0.420: 12 0.420 - 0.525: 6 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CB ILE N 83 " pdb=" CA ILE N 83 " pdb=" CG1 ILE N 83 " pdb=" CG2 ILE N 83 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CB ILE L 83 " pdb=" CA ILE L 83 " pdb=" CG1 ILE L 83 " pdb=" CG2 ILE L 83 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CB ILE D 534 " pdb=" CA ILE D 534 " pdb=" CG1 ILE D 534 " pdb=" CG2 ILE D 534 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 4341 not shown) Planarity restraints: 4947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 83 " -0.033 2.00e-02 2.50e+03 6.60e-02 4.36e+01 pdb=" C THR B 83 " 0.114 2.00e-02 2.50e+03 pdb=" O THR B 83 " -0.042 2.00e-02 2.50e+03 pdb=" N ARG B 84 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 83 " -0.033 2.00e-02 2.50e+03 6.60e-02 4.36e+01 pdb=" C THR D 83 " 0.114 2.00e-02 2.50e+03 pdb=" O THR D 83 " -0.042 2.00e-02 2.50e+03 pdb=" N ARG D 84 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 184 " -0.031 2.00e-02 2.50e+03 6.09e-02 3.70e+01 pdb=" C ASN D 184 " 0.105 2.00e-02 2.50e+03 pdb=" O ASN D 184 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS D 185 " -0.036 2.00e-02 2.50e+03 ... (remaining 4944 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 22 2.08 - 2.78: 6733 2.78 - 3.49: 36788 3.49 - 4.19: 64428 4.19 - 4.90: 106470 Nonbonded interactions: 214441 Sorted by model distance: nonbonded pdb=" O ILE C 29 " pdb=" OG1 THR C 63 " model vdw 1.373 2.440 nonbonded pdb=" O PHE A 137 " pdb=" O LEU A 138 " model vdw 1.437 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR A 122 " model vdw 1.619 2.440 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 122 " model vdw 1.627 2.440 nonbonded pdb=" CG2 VAL A 118 " pdb=" O SER A 136 " model vdw 1.650 3.460 ... (remaining 214436 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 'C' and (resid 27 through 187 or resid 211 through 862)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'H' and resid 2 through 120) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 0.740 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: 5.120 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 68.660 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 28773 Z= 0.387 Angle : 1.410 21.825 38954 Z= 0.812 Chirality : 0.073 0.525 4344 Planarity : 0.009 0.109 4947 Dihedral : 16.520 116.346 10488 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 1.70 % Allowed : 11.71 % Favored : 86.59 % Rotamer: Outliers : 3.86 % Allowed : 11.49 % Favored : 84.65 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 7.35 % Twisted General : 1.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.11), residues: 3528 helix: -3.19 (0.10), residues: 1116 sheet: -2.26 (0.24), residues: 398 loop : -3.30 (0.11), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.004 TRP C 402 HIS 0.024 0.003 HIS D 311 PHE 0.083 0.003 PHE D 176 TYR 0.059 0.003 TYR B 167 ARG 0.012 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 256 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7480 (m) REVERT: A 463 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5371 (p) REVERT: A 586 LEU cc_start: 0.9139 (mp) cc_final: 0.8935 (tt) REVERT: A 598 LEU cc_start: 0.8636 (mt) cc_final: 0.8421 (mt) REVERT: A 723 MET cc_start: 0.6938 (tpt) cc_final: 0.6151 (tpt) REVERT: A 783 MET cc_start: 0.5041 (mtp) cc_final: 0.4836 (mtm) REVERT: A 834 MET cc_start: 0.8006 (tpt) cc_final: 0.7151 (mpp) REVERT: B 54 HIS cc_start: 0.8165 (p-80) cc_final: 0.7687 (p-80) REVERT: B 207 MET cc_start: 0.6494 (mpp) cc_final: 0.5194 (mmm) REVERT: C 411 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5089 (mmt-90) REVERT: C 463 THR cc_start: 0.6370 (OUTLIER) cc_final: 0.5996 (p) REVERT: C 586 LEU cc_start: 0.9245 (mp) cc_final: 0.8919 (tt) REVERT: C 589 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (pp) REVERT: C 723 MET cc_start: 0.6752 (tpt) cc_final: 0.6022 (tpt) REVERT: D 54 HIS cc_start: 0.8240 (p-80) cc_final: 0.7987 (p90) REVERT: D 207 MET cc_start: 0.6491 (mpp) cc_final: 0.4912 (mmm) REVERT: D 386 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.3730 (mmm) REVERT: D 829 MET cc_start: 0.8385 (tmm) cc_final: 0.8166 (tmm) REVERT: H 3 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8420 (mmmt) REVERT: H 34 MET cc_start: 0.5985 (mmm) cc_final: 0.5172 (mmm) REVERT: L 22 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5052 (t) REVERT: L 28 ASP cc_start: 0.6889 (m-30) cc_final: 0.6181 (p0) REVERT: L 82 ASP cc_start: 0.4291 (p0) cc_final: 0.3621 (p0) REVERT: M 3 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7768 (tptt) REVERT: M 34 MET cc_start: 0.7112 (mmm) cc_final: 0.6750 (mmm) REVERT: M 80 TYR cc_start: 0.7544 (m-80) cc_final: 0.6904 (m-80) REVERT: N 5 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (t) REVERT: N 22 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.6221 (t) REVERT: N 24 LYS cc_start: 0.9162 (mttt) cc_final: 0.8927 (mmmt) REVERT: N 50 TYR cc_start: 0.6699 (m-10) cc_final: 0.6315 (p90) REVERT: N 72 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8064 (m) outliers start: 119 outliers final: 23 residues processed: 362 average time/residue: 0.4146 time to fit residues: 235.4490 Evaluate side-chains 216 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 147 GLN A 425 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 357 GLN B 495 ASN B 656 GLN B 711 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 67 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 147 GLN D 311 HIS D 357 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 656 GLN D 711 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS L 49 HIS L 55 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28773 Z= 0.285 Angle : 0.814 10.040 38954 Z= 0.434 Chirality : 0.048 0.260 4344 Planarity : 0.006 0.101 4947 Dihedral : 7.757 78.823 3854 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.67 % Favored : 89.74 % Rotamer: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.76 % 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: -3.22 (0.12), residues: 3528 helix: -1.18 (0.14), residues: 1154 sheet: -1.64 (0.25), residues: 422 loop : -2.97 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 151 HIS 0.010 0.002 HIS D 311 PHE 0.046 0.002 PHE A 42 TYR 0.024 0.002 TYR B 738 ARG 0.010 0.001 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.6715 (ttp) cc_final: 0.6486 (tmm) REVERT: A 586 LEU cc_start: 0.9289 (mp) cc_final: 0.9089 (tt) REVERT: A 839 MET cc_start: 0.8128 (ppp) cc_final: 0.7821 (ptt) REVERT: B 54 HIS cc_start: 0.8160 (p-80) cc_final: 0.7855 (p-80) REVERT: B 207 MET cc_start: 0.6489 (mpp) cc_final: 0.5457 (mmm) REVERT: B 394 MET cc_start: 0.6210 (ptp) cc_final: 0.5949 (pmm) REVERT: C 155 MET cc_start: 0.6966 (ttp) cc_final: 0.6533 (tmm) REVERT: C 347 MET cc_start: 0.9318 (ptt) cc_final: 0.8947 (ppp) REVERT: C 839 MET cc_start: 0.8191 (ppp) cc_final: 0.7809 (ptt) REVERT: D 54 HIS cc_start: 0.8299 (p-80) cc_final: 0.8087 (p90) REVERT: D 89 MET cc_start: 0.7521 (tpt) cc_final: 0.7276 (tpt) REVERT: D 207 MET cc_start: 0.6756 (mpp) cc_final: 0.5799 (mmm) REVERT: D 394 MET cc_start: 0.5759 (ptp) cc_final: 0.5491 (pmm) REVERT: H 3 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8468 (mmmt) REVERT: H 34 MET cc_start: 0.6659 (mmm) cc_final: 0.5462 (mmm) REVERT: H 80 TYR cc_start: 0.7258 (m-80) cc_final: 0.6623 (m-80) REVERT: H 83 MET cc_start: 0.4101 (mmp) cc_final: 0.2591 (mtm) REVERT: L 28 ASP cc_start: 0.6820 (m-30) cc_final: 0.6082 (p0) REVERT: M 3 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7750 (tptt) REVERT: M 34 MET cc_start: 0.7091 (mmm) cc_final: 0.6476 (mmm) REVERT: M 80 TYR cc_start: 0.7618 (m-80) cc_final: 0.7021 (m-80) REVERT: N 24 LYS cc_start: 0.9201 (mttt) cc_final: 0.8886 (mmmt) outliers start: 6 outliers final: 0 residues processed: 197 average time/residue: 0.4278 time to fit residues: 133.3163 Evaluate side-chains 165 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS B 486 HIS ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 146 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28773 Z= 0.213 Angle : 0.721 9.675 38954 Z= 0.383 Chirality : 0.045 0.210 4344 Planarity : 0.006 0.147 4947 Dihedral : 7.099 66.107 3854 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.69 % Favored : 88.89 % Rotamer: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.67 % 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: -2.49 (0.13), residues: 3528 helix: -0.20 (0.15), residues: 1160 sheet: -1.55 (0.25), residues: 416 loop : -2.71 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 796 HIS 0.008 0.001 HIS B 486 PHE 0.026 0.002 PHE C 137 TYR 0.023 0.002 TYR B 252 ARG 0.011 0.000 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.6973 (ttp) cc_final: 0.6611 (tmm) REVERT: A 839 MET cc_start: 0.8184 (ppp) cc_final: 0.7825 (ptt) REVERT: B 54 HIS cc_start: 0.8222 (p-80) cc_final: 0.7950 (p-80) REVERT: B 89 MET cc_start: 0.7645 (tpt) cc_final: 0.7263 (tpt) REVERT: B 207 MET cc_start: 0.6996 (mpp) cc_final: 0.6161 (mmm) REVERT: B 386 MET cc_start: 0.4492 (mmm) cc_final: 0.3797 (mtp) REVERT: B 394 MET cc_start: 0.5984 (ptp) cc_final: 0.5742 (pmm) REVERT: C 155 MET cc_start: 0.7097 (ttp) cc_final: 0.6643 (tmm) REVERT: C 347 MET cc_start: 0.9159 (ptt) cc_final: 0.8940 (ppp) REVERT: C 839 MET cc_start: 0.8181 (ppp) cc_final: 0.7845 (ptt) REVERT: D 207 MET cc_start: 0.7022 (mpp) cc_final: 0.6208 (mmm) REVERT: D 386 MET cc_start: 0.4095 (mmp) cc_final: 0.3513 (tpp) REVERT: D 394 MET cc_start: 0.5650 (ptp) cc_final: 0.5383 (pmm) REVERT: D 809 MET cc_start: 0.8370 (pmm) cc_final: 0.7408 (tpt) REVERT: H 3 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8090 (tptt) REVERT: H 34 MET cc_start: 0.7264 (mmm) cc_final: 0.6758 (mmm) REVERT: H 80 TYR cc_start: 0.7671 (m-80) cc_final: 0.7237 (m-80) REVERT: L 82 ASP cc_start: 0.3580 (p0) cc_final: 0.2920 (p0) REVERT: M 3 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7768 (tptt) REVERT: M 80 TYR cc_start: 0.7594 (m-80) cc_final: 0.6913 (m-80) REVERT: N 24 LYS cc_start: 0.9190 (mttt) cc_final: 0.8880 (mmmt) outliers start: 2 outliers final: 0 residues processed: 194 average time/residue: 0.4160 time to fit residues: 128.4289 Evaluate side-chains 165 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 10.0000 chunk 242 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 216 optimal weight: 20.0000 chunk 323 optimal weight: 40.0000 chunk 342 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 359 HIS B 495 ASN B 697 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 697 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28773 Z= 0.244 Angle : 0.711 8.416 38954 Z= 0.375 Chirality : 0.044 0.209 4344 Planarity : 0.005 0.070 4947 Dihedral : 6.813 61.224 3854 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.91 % Favored : 88.69 % Rotamer: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.47 % 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: -2.12 (0.14), residues: 3528 helix: 0.27 (0.15), residues: 1172 sheet: -1.58 (0.24), residues: 417 loop : -2.57 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 379 HIS 0.012 0.001 HIS D 54 PHE 0.025 0.002 PHE C 137 TYR 0.020 0.002 TYR H 32 ARG 0.008 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7168 (ttp) cc_final: 0.6700 (tmm) REVERT: A 347 MET cc_start: 0.9197 (ptt) cc_final: 0.8892 (ppp) REVERT: A 375 MET cc_start: 0.8025 (mpp) cc_final: 0.7624 (mpp) REVERT: A 839 MET cc_start: 0.7991 (ppp) cc_final: 0.7609 (ptt) REVERT: B 89 MET cc_start: 0.7690 (tpt) cc_final: 0.7420 (tpt) REVERT: B 207 MET cc_start: 0.6985 (mpp) cc_final: 0.6127 (mmm) REVERT: B 809 MET cc_start: 0.8137 (pmm) cc_final: 0.7318 (tpt) REVERT: C 155 MET cc_start: 0.7403 (ttp) cc_final: 0.6784 (tmm) REVERT: D 142 MET cc_start: 0.7172 (mpp) cc_final: 0.6938 (mpp) REVERT: D 207 MET cc_start: 0.6988 (mpp) cc_final: 0.6165 (mmm) REVERT: D 809 MET cc_start: 0.8479 (pmm) cc_final: 0.7229 (tpt) REVERT: D 829 MET cc_start: 0.8159 (tmm) cc_final: 0.7867 (tmm) REVERT: H 3 LYS cc_start: 0.8924 (mmtt) cc_final: 0.7987 (tptt) REVERT: H 34 MET cc_start: 0.7246 (mmm) cc_final: 0.6827 (mmm) REVERT: H 80 TYR cc_start: 0.7380 (m-80) cc_final: 0.6998 (m-80) REVERT: L 82 ASP cc_start: 0.3881 (p0) cc_final: 0.3054 (p0) REVERT: M 3 LYS cc_start: 0.8660 (mmtt) cc_final: 0.7930 (tptt) REVERT: M 34 MET cc_start: 0.7161 (tpt) cc_final: 0.6796 (tpt) REVERT: M 80 TYR cc_start: 0.7519 (m-80) cc_final: 0.6943 (m-80) REVERT: N 24 LYS cc_start: 0.9168 (mttt) cc_final: 0.8868 (mmmt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.4130 time to fit residues: 125.6837 Evaluate side-chains 165 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 291 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 217 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28773 Z= 0.182 Angle : 0.675 8.569 38954 Z= 0.353 Chirality : 0.045 0.270 4344 Planarity : 0.005 0.068 4947 Dihedral : 6.576 56.896 3854 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.63 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.50 % 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: -1.91 (0.14), residues: 3528 helix: 0.55 (0.16), residues: 1162 sheet: -1.49 (0.25), residues: 409 loop : -2.48 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 379 HIS 0.004 0.001 HIS C 171 PHE 0.024 0.001 PHE C 137 TYR 0.018 0.002 TYR D 507 ARG 0.004 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7572 (ttp) cc_final: 0.7013 (tmm) REVERT: A 347 MET cc_start: 0.9146 (ptt) cc_final: 0.8886 (ppp) REVERT: A 375 MET cc_start: 0.7996 (mpp) cc_final: 0.7627 (mpp) REVERT: A 839 MET cc_start: 0.7763 (ppp) cc_final: 0.7387 (ptt) REVERT: B 54 HIS cc_start: 0.8027 (p-80) cc_final: 0.7688 (p-80) REVERT: B 89 MET cc_start: 0.7664 (tpt) cc_final: 0.7396 (tpt) REVERT: B 207 MET cc_start: 0.6725 (mpp) cc_final: 0.6071 (mmm) REVERT: B 307 MET cc_start: 0.8183 (ptt) cc_final: 0.7875 (ptm) REVERT: B 386 MET cc_start: 0.4630 (mmp) cc_final: 0.4336 (mmm) REVERT: B 809 MET cc_start: 0.8586 (pmm) cc_final: 0.7409 (tpt) REVERT: C 155 MET cc_start: 0.7494 (ttp) cc_final: 0.6791 (tmm) REVERT: C 523 MET cc_start: 0.7415 (ptm) cc_final: 0.6918 (ppp) REVERT: D 207 MET cc_start: 0.6844 (mpp) cc_final: 0.6194 (mmm) REVERT: D 307 MET cc_start: 0.7609 (ptt) cc_final: 0.6890 (ptt) REVERT: D 386 MET cc_start: 0.4486 (mmm) cc_final: 0.3835 (tpp) REVERT: D 809 MET cc_start: 0.8848 (pmm) cc_final: 0.7268 (tpt) REVERT: H 34 MET cc_start: 0.7660 (mmm) cc_final: 0.7085 (mmm) REVERT: H 80 TYR cc_start: 0.7387 (m-80) cc_final: 0.6772 (m-80) REVERT: L 28 ASP cc_start: 0.6222 (m-30) cc_final: 0.5680 (p0) REVERT: L 82 ASP cc_start: 0.3634 (p0) cc_final: 0.2164 (p0) REVERT: M 3 LYS cc_start: 0.8713 (mmtt) cc_final: 0.7832 (tptt) REVERT: M 34 MET cc_start: 0.6939 (tpt) cc_final: 0.6604 (tpt) REVERT: M 80 TYR cc_start: 0.7519 (m-80) cc_final: 0.6954 (m-80) REVERT: N 24 LYS cc_start: 0.9149 (mttt) cc_final: 0.8877 (mmmt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.4369 time to fit residues: 132.9932 Evaluate side-chains 165 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 3.9990 chunk 308 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 342 optimal weight: 50.0000 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 740 GLN B 60 HIS ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 740 GLN D 218 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN M 84 ASN N 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28773 Z= 0.247 Angle : 0.704 8.599 38954 Z= 0.372 Chirality : 0.044 0.187 4344 Planarity : 0.005 0.098 4947 Dihedral : 6.550 54.768 3854 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.68 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 3.68 % Twisted General : 0.50 % 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: -1.84 (0.14), residues: 3528 helix: 0.62 (0.16), residues: 1186 sheet: -1.38 (0.26), residues: 390 loop : -2.50 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 379 HIS 0.006 0.001 HIS A 392 PHE 0.022 0.002 PHE C 137 TYR 0.025 0.002 TYR D 254 ARG 0.007 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7640 (ttp) cc_final: 0.7250 (tmm) REVERT: A 347 MET cc_start: 0.9186 (ptt) cc_final: 0.8956 (ppp) REVERT: A 375 MET cc_start: 0.8159 (mpp) cc_final: 0.7691 (mpp) REVERT: B 54 HIS cc_start: 0.8177 (p-80) cc_final: 0.7825 (p-80) REVERT: B 89 MET cc_start: 0.7701 (tpt) cc_final: 0.7479 (tpt) REVERT: B 207 MET cc_start: 0.6873 (mpp) cc_final: 0.6164 (mmm) REVERT: B 386 MET cc_start: 0.4967 (mmp) cc_final: 0.3502 (mtp) REVERT: B 809 MET cc_start: 0.8892 (pmm) cc_final: 0.7776 (tpt) REVERT: B 829 MET cc_start: 0.8357 (tmm) cc_final: 0.8089 (tmm) REVERT: C 155 MET cc_start: 0.7585 (ttp) cc_final: 0.7090 (tmm) REVERT: C 523 MET cc_start: 0.7465 (ptm) cc_final: 0.7058 (ppp) REVERT: D 207 MET cc_start: 0.7316 (mpp) cc_final: 0.6946 (mmm) REVERT: D 809 MET cc_start: 0.8880 (pmm) cc_final: 0.7553 (tpt) REVERT: H 3 LYS cc_start: 0.8949 (mmtt) cc_final: 0.7861 (tptt) REVERT: H 34 MET cc_start: 0.7260 (mmm) cc_final: 0.6800 (mmm) REVERT: L 82 ASP cc_start: 0.2768 (p0) cc_final: 0.2241 (p0) REVERT: M 3 LYS cc_start: 0.8627 (mmtt) cc_final: 0.7902 (tptt) REVERT: M 34 MET cc_start: 0.6533 (tpt) cc_final: 0.6158 (tpt) REVERT: N 24 LYS cc_start: 0.9121 (mttt) cc_final: 0.8869 (mmmt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.4072 time to fit residues: 122.6916 Evaluate side-chains 163 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 157 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 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B 159 ASN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN D 159 ASN D 357 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28773 Z= 0.285 Angle : 0.747 12.867 38954 Z= 0.392 Chirality : 0.045 0.187 4344 Planarity : 0.005 0.091 4947 Dihedral : 6.698 55.458 3854 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.33 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.47 % 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: -1.91 (0.14), residues: 3528 helix: 0.57 (0.15), residues: 1184 sheet: -1.53 (0.25), residues: 390 loop : -2.51 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 796 HIS 0.007 0.001 HIS C 171 PHE 0.027 0.002 PHE C 838 TYR 0.047 0.002 TYR B 254 ARG 0.010 0.001 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7666 (ttp) cc_final: 0.7370 (ttp) REVERT: A 375 MET cc_start: 0.8320 (mpp) cc_final: 0.7750 (mpp) REVERT: B 54 HIS cc_start: 0.8241 (p-80) cc_final: 0.7902 (p-80) REVERT: B 142 MET cc_start: 0.7501 (pmm) cc_final: 0.7260 (pmm) REVERT: B 207 MET cc_start: 0.7274 (mpp) cc_final: 0.6730 (mmm) REVERT: B 386 MET cc_start: 0.5799 (mmp) cc_final: 0.4981 (tpp) REVERT: B 809 MET cc_start: 0.8873 (pmm) cc_final: 0.7780 (tpt) REVERT: B 829 MET cc_start: 0.8454 (tmm) cc_final: 0.8127 (tmm) REVERT: C 155 MET cc_start: 0.7700 (ttp) cc_final: 0.7061 (tmm) REVERT: C 415 MET cc_start: 0.8288 (mmm) cc_final: 0.7900 (mmm) REVERT: C 523 MET cc_start: 0.7542 (ptm) cc_final: 0.7127 (ppp) REVERT: D 207 MET cc_start: 0.7360 (mpp) cc_final: 0.6627 (mmm) REVERT: D 809 MET cc_start: 0.8925 (pmm) cc_final: 0.7669 (tpt) REVERT: D 824 MET cc_start: 0.8364 (mmt) cc_final: 0.7565 (mmm) REVERT: H 3 LYS cc_start: 0.9049 (mmtt) cc_final: 0.7736 (tptt) REVERT: H 34 MET cc_start: 0.6782 (mmm) cc_final: 0.6465 (mmm) REVERT: H 80 TYR cc_start: 0.7771 (m-80) cc_final: 0.7297 (m-80) REVERT: L 82 ASP cc_start: 0.2236 (p0) cc_final: 0.1772 (p0) REVERT: M 3 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7777 (tptt) REVERT: M 34 MET cc_start: 0.6776 (tpt) cc_final: 0.6295 (tpt) REVERT: M 67 ARG cc_start: 0.7799 (tmt-80) cc_final: 0.7144 (tpt90) REVERT: M 80 TYR cc_start: 0.7709 (m-80) cc_final: 0.7185 (m-80) REVERT: N 24 LYS cc_start: 0.9215 (mttt) cc_final: 0.8949 (mmmt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.4097 time to fit residues: 125.7874 Evaluate side-chains 167 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 203 optimal weight: 0.0000 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 HIS L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28773 Z= 0.182 Angle : 0.686 10.618 38954 Z= 0.356 Chirality : 0.045 0.160 4344 Planarity : 0.005 0.091 4947 Dihedral : 6.432 53.395 3854 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.14 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.56 % 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: -1.69 (0.14), residues: 3528 helix: 0.77 (0.16), residues: 1180 sheet: -1.31 (0.26), residues: 367 loop : -2.41 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 796 HIS 0.005 0.001 HIS C 171 PHE 0.027 0.002 PHE A 137 TYR 0.034 0.002 TYR B 254 ARG 0.006 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7555 (ttp) cc_final: 0.7087 (tmm) REVERT: A 375 MET cc_start: 0.8268 (mpp) cc_final: 0.7749 (mpp) REVERT: B 142 MET cc_start: 0.7210 (pmm) cc_final: 0.6938 (pmm) REVERT: B 207 MET cc_start: 0.7341 (mpp) cc_final: 0.7054 (mmm) REVERT: B 386 MET cc_start: 0.5650 (mmp) cc_final: 0.4803 (tpp) REVERT: B 654 MET cc_start: 0.7683 (tmm) cc_final: 0.7377 (tmm) REVERT: B 809 MET cc_start: 0.8961 (pmm) cc_final: 0.7769 (tpt) REVERT: B 829 MET cc_start: 0.8420 (tmm) cc_final: 0.8132 (tmm) REVERT: C 155 MET cc_start: 0.7575 (ttp) cc_final: 0.7170 (tmm) REVERT: C 415 MET cc_start: 0.8280 (mmm) cc_final: 0.7917 (mmm) REVERT: C 523 MET cc_start: 0.7415 (ptm) cc_final: 0.7094 (ppp) REVERT: C 586 LEU cc_start: 0.9330 (tt) cc_final: 0.8837 (tt) REVERT: D 207 MET cc_start: 0.7336 (mpp) cc_final: 0.7050 (mmm) REVERT: D 809 MET cc_start: 0.8911 (pmm) cc_final: 0.7754 (tpt) REVERT: D 824 MET cc_start: 0.8245 (mmt) cc_final: 0.7527 (mmm) REVERT: H 3 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8257 (mmmt) REVERT: H 34 MET cc_start: 0.7187 (mmm) cc_final: 0.6714 (mmm) REVERT: H 80 TYR cc_start: 0.7810 (m-80) cc_final: 0.7441 (m-80) REVERT: H 112 TRP cc_start: 0.7396 (p-90) cc_final: 0.7128 (p-90) REVERT: L 50 TYR cc_start: 0.6010 (m-80) cc_final: 0.5774 (m-80) REVERT: L 82 ASP cc_start: 0.2112 (p0) cc_final: 0.1885 (p0) REVERT: M 3 LYS cc_start: 0.8597 (mmtt) cc_final: 0.7679 (tptt) REVERT: M 34 MET cc_start: 0.6717 (tpt) cc_final: 0.6261 (tpt) REVERT: M 80 TYR cc_start: 0.7751 (m-80) cc_final: 0.7495 (m-80) REVERT: N 24 LYS cc_start: 0.9218 (mttt) cc_final: 0.8953 (mmmt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.4606 time to fit residues: 141.5145 Evaluate side-chains 169 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 298 optimal weight: 7.9990 chunk 317 optimal weight: 40.0000 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 0.0070 chunk 249 optimal weight: 7.9990 chunk 97 optimal weight: 0.0010 chunk 287 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 overall best weight: 2.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28773 Z= 0.194 Angle : 0.688 10.912 38954 Z= 0.356 Chirality : 0.044 0.203 4344 Planarity : 0.005 0.088 4947 Dihedral : 6.314 52.613 3854 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.25 % Favored : 88.61 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.50 % 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: -1.60 (0.14), residues: 3528 helix: 0.88 (0.16), residues: 1180 sheet: -1.33 (0.25), residues: 377 loop : -2.37 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 796 HIS 0.007 0.001 HIS C 162 PHE 0.021 0.002 PHE A 137 TYR 0.022 0.002 TYR C 668 ARG 0.005 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7592 (ttp) cc_final: 0.7078 (tmm) REVERT: A 375 MET cc_start: 0.8288 (mpp) cc_final: 0.7720 (mpp) REVERT: B 142 MET cc_start: 0.6998 (pmm) cc_final: 0.6625 (pmm) REVERT: B 207 MET cc_start: 0.7343 (mpp) cc_final: 0.6654 (mmm) REVERT: B 386 MET cc_start: 0.5616 (mmp) cc_final: 0.4770 (tpp) REVERT: B 654 MET cc_start: 0.7769 (tmm) cc_final: 0.7469 (tmm) REVERT: B 809 MET cc_start: 0.8933 (pmm) cc_final: 0.7754 (tpt) REVERT: B 829 MET cc_start: 0.8402 (tmm) cc_final: 0.8122 (tmm) REVERT: C 155 MET cc_start: 0.7595 (ttp) cc_final: 0.7264 (tmm) REVERT: C 415 MET cc_start: 0.8337 (mmm) cc_final: 0.7959 (mmm) REVERT: C 523 MET cc_start: 0.7546 (ptm) cc_final: 0.7051 (ppp) REVERT: D 207 MET cc_start: 0.7415 (mpp) cc_final: 0.6746 (mmm) REVERT: D 565 MET cc_start: 0.8201 (mmt) cc_final: 0.7978 (tpp) REVERT: D 809 MET cc_start: 0.8906 (pmm) cc_final: 0.7757 (tpt) REVERT: D 824 MET cc_start: 0.8237 (mmt) cc_final: 0.7547 (mmm) REVERT: D 829 MET cc_start: 0.8423 (tmm) cc_final: 0.8153 (tmm) REVERT: H 3 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8267 (mmmt) REVERT: H 80 TYR cc_start: 0.7915 (m-80) cc_final: 0.7545 (m-80) REVERT: H 98 ARG cc_start: 0.4497 (ttp-170) cc_final: 0.4219 (ttp-170) REVERT: H 112 TRP cc_start: 0.7355 (p-90) cc_final: 0.7093 (p-90) REVERT: L 82 ASP cc_start: 0.2171 (p0) cc_final: 0.1736 (p0) REVERT: M 3 LYS cc_start: 0.8461 (mmtt) cc_final: 0.7663 (tptt) REVERT: M 34 MET cc_start: 0.6741 (tpt) cc_final: 0.6351 (tpt) REVERT: M 80 TYR cc_start: 0.7907 (m-80) cc_final: 0.7679 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.4423 time to fit residues: 138.5952 Evaluate side-chains 167 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 8.9990 chunk 336 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 352 optimal weight: 0.7980 chunk 324 optimal weight: 50.0000 chunk 280 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 216 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 HIS L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28773 Z= 0.164 Angle : 0.679 10.098 38954 Z= 0.350 Chirality : 0.045 0.189 4344 Planarity : 0.005 0.089 4947 Dihedral : 6.123 51.167 3854 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.94 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.47 % 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: -1.50 (0.14), residues: 3528 helix: 0.97 (0.16), residues: 1170 sheet: -1.20 (0.26), residues: 367 loop : -2.30 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 796 HIS 0.008 0.001 HIS A 67 PHE 0.021 0.001 PHE A 137 TYR 0.021 0.002 TYR D 731 ARG 0.006 0.000 ARG M 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8217 (mpp) cc_final: 0.7697 (mpp) REVERT: B 142 MET cc_start: 0.6817 (pmm) cc_final: 0.6499 (pmm) REVERT: B 207 MET cc_start: 0.7336 (mpp) cc_final: 0.6707 (mmm) REVERT: B 386 MET cc_start: 0.5521 (mmp) cc_final: 0.4666 (tpp) REVERT: B 565 MET cc_start: 0.7929 (mmt) cc_final: 0.7420 (tpt) REVERT: B 654 MET cc_start: 0.7824 (tmm) cc_final: 0.7509 (tmm) REVERT: B 809 MET cc_start: 0.8864 (pmm) cc_final: 0.7668 (tpt) REVERT: B 829 MET cc_start: 0.8354 (tmm) cc_final: 0.8136 (tmm) REVERT: C 155 MET cc_start: 0.7721 (ttp) cc_final: 0.7410 (tmm) REVERT: C 415 MET cc_start: 0.8359 (mmm) cc_final: 0.7988 (mmm) REVERT: C 523 MET cc_start: 0.7717 (ptm) cc_final: 0.7113 (ppp) REVERT: D 207 MET cc_start: 0.7369 (mpp) cc_final: 0.6793 (mmm) REVERT: D 561 MET cc_start: 0.8736 (pmm) cc_final: 0.8517 (pmm) REVERT: D 565 MET cc_start: 0.8232 (mmt) cc_final: 0.7864 (tpp) REVERT: D 654 MET cc_start: 0.7993 (ppp) cc_final: 0.7664 (tmm) REVERT: D 809 MET cc_start: 0.8951 (pmm) cc_final: 0.7741 (tpt) REVERT: D 829 MET cc_start: 0.8400 (tmm) cc_final: 0.8145 (tmm) REVERT: H 3 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8261 (mmmt) REVERT: H 98 ARG cc_start: 0.4425 (ttp-170) cc_final: 0.4207 (ttp-170) REVERT: L 28 ASP cc_start: 0.5060 (m-30) cc_final: 0.3466 (t70) REVERT: L 82 ASP cc_start: 0.2511 (p0) cc_final: 0.1990 (p0) REVERT: M 3 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7632 (tptt) REVERT: M 34 MET cc_start: 0.6673 (tpt) cc_final: 0.6264 (tpt) REVERT: M 80 TYR cc_start: 0.7923 (m-80) cc_final: 0.7704 (m-80) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.4135 time to fit residues: 127.7582 Evaluate side-chains 168 residues out of total 3092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 86 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 HIS L 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.045713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032591 restraints weight = 376763.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033174 restraints weight = 239676.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.033535 restraints weight = 178828.482| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28773 Z= 0.235 Angle : 0.707 11.174 38954 Z= 0.367 Chirality : 0.045 0.203 4344 Planarity : 0.005 0.086 4947 Dihedral : 6.224 51.015 3854 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.16 % Favored : 87.70 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3528 helix: 1.02 (0.16), residues: 1172 sheet: -1.44 (0.25), residues: 375 loop : -2.26 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 796 HIS 0.005 0.001 HIS C 171 PHE 0.019 0.002 PHE A 137 TYR 0.019 0.002 TYR A 668 ARG 0.006 0.000 ARG M 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.92 seconds wall clock time: 90 minutes 5.82 seconds (5405.82 seconds total)