Starting phenix.real_space_refine on Mon Mar 25 10:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hra_34965/03_2024/8hra_34965_neut_updated.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 220 5.16 5 C 30260 2.51 5 N 8313 2.21 5 O 9290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 890": "OE1" <-> "OE2" Residue "G TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 319": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G GLU 354": "OE1" <-> "OE2" Residue "G GLU 529": "OE1" <-> "OE2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 201": "OE1" <-> "OE2" Residue "H GLU 360": "OE1" <-> "OE2" Residue "H GLU 789": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48146 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6754 Classifications: {'peptide': 847} Link IDs: {'PTRANS': 23, 'TRANS': 823} Chain breaks: 4 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "C" Number of atoms: 6784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6784 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 23, 'TRANS': 828} Chain breaks: 4 Chain: "D" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6757 Classifications: {'peptide': 848} Link IDs: {'PTRANS': 23, 'TRANS': 824} Chain breaks: 4 Chain: "E" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6654 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "G" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "H" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "K" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "M" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.41, per 1000 atoms: 0.51 Number of scatterers: 48146 At special positions: 0 Unit cell: (172.78, 177.02, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 63 15.00 O 9290 8.00 N 8313 7.00 C 30260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.36 Conformation dependent library (CDL) restraints added in 8.0 seconds 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 276 helices and 21 sheets defined 54.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.39 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.701A pdb=" N SER A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.804A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 167 removed outlier: 3.555A pdb=" N LYS A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.715A pdb=" N ASP A 179 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.777A pdb=" N SER A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.536A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.705A pdb=" N LEU A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 376 through 393 removed outlier: 4.074A pdb=" N LYS A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.721A pdb=" N LYS A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.103A pdb=" N SER A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.560A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.765A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.978A pdb=" N ALA A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.521A pdb=" N ASN A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 Processing helix chain 'A' and resid 707 through 726 removed outlier: 5.341A pdb=" N ILE A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 751 Processing helix chain 'A' and resid 771 through 792 removed outlier: 3.769A pdb=" N LEU A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 830 removed outlier: 3.591A pdb=" N GLY A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 No H-bonds generated for 'chain 'A' and resid 835 through 838' Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 852 through 855 No H-bonds generated for 'chain 'A' and resid 852 through 855' Processing helix chain 'A' and resid 865 through 882 removed outlier: 4.104A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 removed outlier: 3.674A pdb=" N ASP A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 896 " --> pdb=" O TRP A 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 896' Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.585A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 3.576A pdb=" N GLY B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 4.208A pdb=" N SER B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.693A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 301 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.751A pdb=" N ALA B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.925A pdb=" N TYR B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 394 removed outlier: 3.903A pdb=" N THR B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 443 through 457 removed outlier: 4.016A pdb=" N PHE B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.805A pdb=" N SER B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 514 removed outlier: 4.267A pdb=" N CYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.682A pdb=" N GLU B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.771A pdb=" N ALA B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.552A pdb=" N SER B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.521A pdb=" N ILE B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 709 through 726 removed outlier: 3.666A pdb=" N LYS B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 748 Processing helix chain 'B' and resid 771 through 793 removed outlier: 3.676A pdb=" N MET B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 830 removed outlier: 3.760A pdb=" N LYS B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 840 through 846 Processing helix chain 'B' and resid 849 through 855 Proline residue: B 853 - end of helix No H-bonds generated for 'chain 'B' and resid 849 through 855' Processing helix chain 'B' and resid 867 through 882 Processing helix chain 'B' and resid 889 through 896 Processing helix chain 'B' and resid 917 through 919 No H-bonds generated for 'chain 'B' and resid 917 through 919' Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 117 through 139 removed outlier: 4.221A pdb=" N ILE C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 166 removed outlier: 3.702A pdb=" N GLU C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.673A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 232 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU C 235 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 237 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 239 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE C 240 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.859A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 301 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.601A pdb=" N ALA C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.639A pdb=" N LYS C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 393 removed outlier: 3.723A pdb=" N GLN C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 443 through 457 removed outlier: 3.869A pdb=" N CYS C 447 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.993A pdb=" N ILE C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 removed outlier: 3.972A pdb=" N CYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 526 through 539 Processing helix chain 'C' and resid 547 through 560 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 598 through 607 removed outlier: 3.658A pdb=" N ALA C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 removed outlier: 3.931A pdb=" N ALA C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 649 removed outlier: 3.589A pdb=" N THR C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 670 Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.883A pdb=" N ASP C 708 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 721 " --> pdb=" O LYS C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 751 removed outlier: 3.718A pdb=" N GLY C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 792 removed outlier: 3.525A pdb=" N PHE C 782 " --> pdb=" O ASN C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 831 removed outlier: 3.693A pdb=" N LYS C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 838 No H-bonds generated for 'chain 'C' and resid 835 through 838' Processing helix chain 'C' and resid 840 through 846 Processing helix chain 'C' and resid 852 through 855 No H-bonds generated for 'chain 'C' and resid 852 through 855' Processing helix chain 'C' and resid 868 through 882 Processing helix chain 'C' and resid 889 through 895 Processing helix chain 'C' and resid 917 through 919 No H-bonds generated for 'chain 'C' and resid 917 through 919' Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.834A pdb=" N ILE D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 166 removed outlier: 3.781A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 removed outlier: 4.366A pdb=" N SER D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 196 through 210 removed outlier: 3.968A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 282 through 301 removed outlier: 3.542A pdb=" N GLN D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 376 through 393 removed outlier: 4.196A pdb=" N LYS D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.636A pdb=" N GLY D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 443 through 457 removed outlier: 4.048A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 451 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.042A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 514 removed outlier: 4.076A pdb=" N CYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 527 through 538 Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.759A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 607 Processing helix chain 'D' and resid 623 through 634 removed outlier: 3.785A pdb=" N ALA D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 649 removed outlier: 4.031A pdb=" N THR D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 removed outlier: 3.851A pdb=" N MET D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 670 " --> pdb=" O ARG D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 No H-bonds generated for 'chain 'D' and resid 702 through 705' Processing helix chain 'D' and resid 707 through 726 removed outlier: 3.686A pdb=" N ASN D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 753 Processing helix chain 'D' and resid 771 through 792 removed outlier: 3.591A pdb=" N PHE D 782 " --> pdb=" O ASN D 778 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 786 " --> pdb=" O PHE D 782 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 830 Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 840 through 846 Processing helix chain 'D' and resid 852 through 856 removed outlier: 4.243A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 852 through 856' Processing helix chain 'D' and resid 865 through 882 removed outlier: 4.056A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP D 879 " --> pdb=" O ASN D 875 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 880 " --> pdb=" O LYS D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 895 Processing helix chain 'D' and resid 917 through 919 No H-bonds generated for 'chain 'D' and resid 917 through 919' Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.900A pdb=" N ILE E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 121 through 140 removed outlier: 3.561A pdb=" N TYR E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 168 removed outlier: 3.697A pdb=" N HIS E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N HIS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.496A pdb=" N SER E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 179 " --> pdb=" O TYR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 229 through 239 removed outlier: 3.659A pdb=" N GLU E 235 " --> pdb=" O ASP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 4.116A pdb=" N GLN E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 299 removed outlier: 3.550A pdb=" N GLN E 296 " --> pdb=" O HIS E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.661A pdb=" N VAL E 317 " --> pdb=" O MET E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 317' Processing helix chain 'E' and resid 344 through 355 removed outlier: 3.634A pdb=" N ALA E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 372 removed outlier: 3.751A pdb=" N TYR E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 394 removed outlier: 3.957A pdb=" N TYR E 391 " --> pdb=" O TYR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 457 removed outlier: 3.693A pdb=" N PHE E 451 " --> pdb=" O CYS E 447 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 473 through 489 removed outlier: 3.826A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 503 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 526 through 539 removed outlier: 3.937A pdb=" N GLN E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 531 " --> pdb=" O LYS E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 removed outlier: 3.823A pdb=" N ALA E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 566 No H-bonds generated for 'chain 'E' and resid 564 through 566' Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 623 through 632 Processing helix chain 'E' and resid 640 through 646 Processing helix chain 'E' and resid 702 through 704 No H-bonds generated for 'chain 'E' and resid 702 through 704' Processing helix chain 'E' and resid 707 through 723 removed outlier: 3.638A pdb=" N ASN E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 755 removed outlier: 3.798A pdb=" N ASN E 747 " --> pdb=" O PHE E 743 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS E 753 " --> pdb=" O ALA E 749 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR E 754 " --> pdb=" O ASP E 750 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG E 755 " --> pdb=" O GLN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 793 Processing helix chain 'E' and resid 815 through 830 removed outlier: 4.008A pdb=" N LYS E 820 " --> pdb=" O GLU E 816 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 838 No H-bonds generated for 'chain 'E' and resid 835 through 838' Processing helix chain 'E' and resid 840 through 846 Processing helix chain 'E' and resid 849 through 855 Proline residue: E 853 - end of helix No H-bonds generated for 'chain 'E' and resid 849 through 855' Processing helix chain 'E' and resid 858 through 860 No H-bonds generated for 'chain 'E' and resid 858 through 860' Processing helix chain 'E' and resid 867 through 882 Processing helix chain 'E' and resid 889 through 896 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 121 through 139 Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.588A pdb=" N GLU G 151 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 180 removed outlier: 3.764A pdb=" N SER G 178 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 228 through 239 removed outlier: 3.515A pdb=" N TRP G 231 " --> pdb=" O ASP G 228 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU G 235 " --> pdb=" O ASP G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.582A pdb=" N GLY G 263 " --> pdb=" O GLN G 259 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU G 267 " --> pdb=" O GLY G 263 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 280 through 301 removed outlier: 3.544A pdb=" N ARG G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR G 288 " --> pdb=" O ALA G 284 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL G 290 " --> pdb=" O ARG G 286 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU G 291 " --> pdb=" O GLY G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 313 through 317 Processing helix chain 'G' and resid 344 through 355 Processing helix chain 'G' and resid 364 through 372 removed outlier: 3.525A pdb=" N VAL G 368 " --> pdb=" O ALA G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 394 removed outlier: 3.878A pdb=" N TYR G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 432 Processing helix chain 'G' and resid 443 through 457 removed outlier: 3.760A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE G 451 " --> pdb=" O CYS G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 473 through 489 removed outlier: 4.315A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR G 481 " --> pdb=" O ASN G 477 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 483 " --> pdb=" O SER G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 502 removed outlier: 3.842A pdb=" N MET G 500 " --> pdb=" O LYS G 496 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 501 " --> pdb=" O PHE G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 514 Processing helix chain 'G' and resid 525 through 539 Processing helix chain 'G' and resid 547 through 560 removed outlier: 3.668A pdb=" N ASN G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 566 No H-bonds generated for 'chain 'G' and resid 564 through 566' Processing helix chain 'G' and resid 598 through 607 removed outlier: 3.958A pdb=" N ALA G 603 " --> pdb=" O ALA G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 634 Processing helix chain 'G' and resid 639 through 647 removed outlier: 3.615A pdb=" N ILE G 642 " --> pdb=" O ARG G 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 703 through 726 removed outlier: 4.515A pdb=" N PHE G 706 " --> pdb=" O ALA G 703 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP G 708 " --> pdb=" O GLU G 705 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 710 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 720 " --> pdb=" O LEU G 717 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 723 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU G 724 " --> pdb=" O ASN G 721 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G 725 " --> pdb=" O GLU G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 751 removed outlier: 3.542A pdb=" N GLY G 735 " --> pdb=" O ALA G 731 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER G 739 " --> pdb=" O GLY G 735 " (cutoff:3.500A) Processing helix chain 'G' and resid 771 through 793 removed outlier: 3.594A pdb=" N SER G 791 " --> pdb=" O LEU G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 831 Processing helix chain 'G' and resid 835 through 838 No H-bonds generated for 'chain 'G' and resid 835 through 838' Processing helix chain 'G' and resid 840 through 846 Processing helix chain 'G' and resid 852 through 855 No H-bonds generated for 'chain 'G' and resid 852 through 855' Processing helix chain 'G' and resid 858 through 860 No H-bonds generated for 'chain 'G' and resid 858 through 860' Processing helix chain 'G' and resid 867 through 882 removed outlier: 3.817A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 889 through 897 Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.547A pdb=" N ASP H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 94 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 121 through 140 removed outlier: 3.618A pdb=" N MET H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 166 removed outlier: 4.142A pdb=" N LYS H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 179 removed outlier: 3.599A pdb=" N SER H 178 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 196 through 211 Processing helix chain 'H' and resid 230 through 238 Processing helix chain 'H' and resid 254 through 266 removed outlier: 4.441A pdb=" N GLN H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 No H-bonds generated for 'chain 'H' and resid 271 through 274' Processing helix chain 'H' and resid 280 through 301 removed outlier: 3.513A pdb=" N MET H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL H 290 " --> pdb=" O ARG H 286 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 313 through 317 Processing helix chain 'H' and resid 344 through 353 Processing helix chain 'H' and resid 362 through 373 removed outlier: 3.793A pdb=" N TYR H 367 " --> pdb=" O ASP H 363 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 368 " --> pdb=" O ALA H 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 394 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 432 removed outlier: 3.800A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 457 Processing helix chain 'H' and resid 463 through 465 No H-bonds generated for 'chain 'H' and resid 463 through 465' Processing helix chain 'H' and resid 473 through 489 removed outlier: 3.702A pdb=" N ILE H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR H 481 " --> pdb=" O ASN H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 503 Processing helix chain 'H' and resid 506 through 514 Processing helix chain 'H' and resid 527 through 539 Processing helix chain 'H' and resid 547 through 560 removed outlier: 3.673A pdb=" N ASN H 552 " --> pdb=" O SER H 548 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 553 " --> pdb=" O HIS H 549 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 566 No H-bonds generated for 'chain 'H' and resid 564 through 566' Processing helix chain 'H' and resid 593 through 595 No H-bonds generated for 'chain 'H' and resid 593 through 595' Processing helix chain 'H' and resid 601 through 607 Processing helix chain 'H' and resid 622 through 635 removed outlier: 3.605A pdb=" N ILE H 626 " --> pdb=" O VAL H 622 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS H 635 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 645 Processing helix chain 'H' and resid 702 through 726 removed outlier: 3.962A pdb=" N SER H 707 " --> pdb=" O ALA H 703 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP H 708 " --> pdb=" O THR H 704 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 709 " --> pdb=" O GLU H 705 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU H 722 " --> pdb=" O LYS H 718 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 723 " --> pdb=" O ASN H 719 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE H 725 " --> pdb=" O ASN H 721 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY H 726 " --> pdb=" O GLU H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 731 through 751 Processing helix chain 'H' and resid 771 through 793 removed outlier: 3.710A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 786 " --> pdb=" O PHE H 782 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 787 " --> pdb=" O LEU H 783 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 789 " --> pdb=" O ALA H 785 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER H 791 " --> pdb=" O LEU H 787 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 792 " --> pdb=" O VAL H 788 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 830 Processing helix chain 'H' and resid 835 through 838 No H-bonds generated for 'chain 'H' and resid 835 through 838' Processing helix chain 'H' and resid 840 through 846 Processing helix chain 'H' and resid 849 through 855 Proline residue: H 853 - end of helix No H-bonds generated for 'chain 'H' and resid 849 through 855' Processing helix chain 'H' and resid 867 through 882 Processing helix chain 'H' and resid 889 through 897 Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 71 through 75 removed outlier: 8.571A pdb=" N PHE A 72 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 248 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL A 74 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 250 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.634A pdb=" N CYS A 655 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 14 through 17 Processing sheet with id= E, first strand: chain 'B' and resid 307 through 309 removed outlier: 8.254A pdb=" N ILE B 308 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE B 73 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N PHE B 72 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 248 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 74 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA B 250 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 216 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 249 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 218 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 251 " --> pdb=" O ILE B 218 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 573 through 575 removed outlier: 3.507A pdb=" N VAL B 574 " --> pdb=" O CYS B 620 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 609 " --> pdb=" O PHE B 619 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 14 through 16 Processing sheet with id= H, first strand: chain 'C' and resid 71 through 75 removed outlier: 8.671A pdb=" N PHE C 72 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 248 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C 74 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 250 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 616 through 620 removed outlier: 3.592A pdb=" N ALA C 612 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 14 through 16 Processing sheet with id= K, first strand: chain 'D' and resid 307 through 309 removed outlier: 7.992A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N PHE D 72 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 248 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL D 74 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA D 250 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 216 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL D 249 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 218 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR D 251 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 616 through 619 removed outlier: 3.617A pdb=" N ALA D 612 " --> pdb=" O CYS D 655 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 14 through 17 Processing sheet with id= N, first strand: chain 'E' and resid 71 through 74 removed outlier: 8.304A pdb=" N PHE E 72 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL E 248 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL E 74 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA E 250 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 105 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 573 through 576 removed outlier: 4.401A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 14 through 17 Processing sheet with id= Q, first strand: chain 'G' and resid 307 through 309 removed outlier: 8.596A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE G 72 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL G 248 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL G 74 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA G 250 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE G 220 " --> pdb=" O THR G 251 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 609 through 611 removed outlier: 3.517A pdb=" N SER G 609 " --> pdb=" O PHE G 619 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE G 619 " --> pdb=" O SER G 609 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= T, first strand: chain 'H' and resid 71 through 75 removed outlier: 8.084A pdb=" N PHE H 72 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL H 248 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL H 74 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA H 250 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL H 249 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE H 218 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 609 through 611 removed outlier: 3.523A pdb=" N SER H 609 " --> pdb=" O PHE H 619 " (cutoff:3.500A) 1927 hydrogen bonds defined for protein. 5532 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: 16.87 Time building geometry restraints manager: 19.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15489 1.34 - 1.46: 6878 1.46 - 1.58: 26257 1.58 - 1.70: 116 1.70 - 1.82: 335 Bond restraints: 49075 Sorted by residual: bond pdb=" N LEU D 599 " pdb=" CA LEU D 599 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.23e-02 6.61e+03 1.20e+01 bond pdb=" N ILE D 593 " pdb=" CA ILE D 593 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.44e+00 bond pdb=" N GLU G 279 " pdb=" CA GLU G 279 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.43e+00 bond pdb=" N ASN D 597 " pdb=" CA ASN D 597 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.97e+00 bond pdb=" N GLU D 596 " pdb=" CA GLU D 596 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.66e+00 ... (remaining 49070 not shown) Histogram of bond angle deviations from ideal: 98.34 - 106.66: 1206 106.66 - 114.97: 29950 114.97 - 123.29: 33654 123.29 - 131.60: 1560 131.60 - 139.91: 81 Bond angle restraints: 66451 Sorted by residual: angle pdb=" N ALA D 600 " pdb=" CA ALA D 600 " pdb=" C ALA D 600 " ideal model delta sigma weight residual 113.55 106.29 7.26 1.26e+00 6.30e-01 3.32e+01 angle pdb=" N VAL E 622 " pdb=" CA VAL E 622 " pdb=" C VAL E 622 " ideal model delta sigma weight residual 113.53 108.20 5.33 9.80e-01 1.04e+00 2.95e+01 angle pdb=" N LYS A 136 " pdb=" CA LYS A 136 " pdb=" C LYS A 136 " ideal model delta sigma weight residual 111.14 105.46 5.68 1.08e+00 8.57e-01 2.77e+01 angle pdb=" N VAL E 814 " pdb=" CA VAL E 814 " pdb=" C VAL E 814 " ideal model delta sigma weight residual 113.20 108.75 4.45 9.60e-01 1.09e+00 2.15e+01 angle pdb=" CA GLY D 598 " pdb=" C GLY D 598 " pdb=" O GLY D 598 " ideal model delta sigma weight residual 121.41 117.69 3.72 8.80e-01 1.29e+00 1.79e+01 ... (remaining 66446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 26512 17.98 - 35.96: 2848 35.96 - 53.94: 480 53.94 - 71.92: 141 71.92 - 89.89: 63 Dihedral angle restraints: 30044 sinusoidal: 12842 harmonic: 17202 Sorted by residual: dihedral pdb=" CA ILE E 223 " pdb=" C ILE E 223 " pdb=" N ASP E 224 " pdb=" CA ASP E 224 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLU H 789 " pdb=" C GLU H 789 " pdb=" N GLU H 790 " pdb=" CA GLU H 790 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU B 187 " pdb=" C LEU B 187 " pdb=" N ASP B 188 " pdb=" CA ASP B 188 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 30041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 5977 0.046 - 0.091: 1249 0.091 - 0.137: 254 0.137 - 0.182: 19 0.182 - 0.228: 6 Chirality restraints: 7505 Sorted by residual: chirality pdb=" CA LYS A 136 " pdb=" N LYS A 136 " pdb=" C LYS A 136 " pdb=" CB LYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LEU A 137 " pdb=" N LEU A 137 " pdb=" C LEU A 137 " pdb=" CB LEU A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP D 594 " pdb=" N ASP D 594 " pdb=" C ASP D 594 " pdb=" CB ASP D 594 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 7502 not shown) Planarity restraints: 8334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 374 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 375 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 119 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 120 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 120 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 120 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 140 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C TYR A 140 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR A 140 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP A 141 " 0.010 2.00e-02 2.50e+03 ... (remaining 8331 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5525 2.75 - 3.28: 48618 3.28 - 3.82: 73826 3.82 - 4.36: 89198 4.36 - 4.90: 151672 Nonbonded interactions: 368839 Sorted by model distance: nonbonded pdb=" OE2 GLU B 816 " pdb=" O2' A M 5 " model vdw 2.207 2.440 nonbonded pdb=" O MET A 132 " pdb=" CG LYS A 136 " model vdw 2.208 3.440 nonbonded pdb=" OH TYR B 189 " pdb=" OE1 GLU B 202 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU H 816 " pdb=" O2' A L 5 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLN B 513 " pdb=" OH TYR B 742 " model vdw 2.222 2.440 ... (remaining 368834 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' and (resid 13 through 95 or resid 102 through 517 or resid 524 throug \ h 663 or resid 667 or resid 704 through 897 or resid 907 through 934)) selection = (chain 'B' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'C' and (resid 13 through 49 or resid 70 through 95 or resid 102 through \ 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'D' and (resid 13 through 95 or resid 102 through 517 or resid 524 throug \ h 663 or resid 667 or resid 704 through 934)) selection = (chain 'E' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'G' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'H' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 663 or resid 703 through 897 or resid 907 through 934)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.040 Extract box with map and model: 10.030 Check model and map are aligned: 0.680 Set scattering table: 0.430 Process input model: 118.900 Find NCS groups from input model: 4.040 Set up NCS constraints: 0.230 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.003 0.043 49075 Z= 0.207 Angle : 0.499 8.332 66451 Z= 0.287 Chirality : 0.039 0.228 7505 Planarity : 0.003 0.048 8334 Dihedral : 15.369 89.894 18884 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5799 helix: 0.56 (0.09), residues: 3105 sheet: 0.60 (0.36), residues: 259 loop : -1.04 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 738 HIS 0.010 0.001 HIS D 118 PHE 0.013 0.001 PHE C 227 TYR 0.017 0.001 TYR D 146 ARG 0.008 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 529 time to evaluate : 6.252 Fit side-chains revert: symmetry clash REVERT: B 313 MET cc_start: 0.8996 (tpp) cc_final: 0.8752 (tpp) REVERT: B 525 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7755 (tpp-160) REVERT: C 132 MET cc_start: 0.8214 (tmm) cc_final: 0.7953 (tpp) REVERT: C 436 TYR cc_start: 0.8320 (p90) cc_final: 0.7132 (p90) REVERT: G 273 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8854 (tp) REVERT: G 789 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7654 (mm-30) REVERT: G 861 ILE cc_start: 0.7867 (mm) cc_final: 0.7638 (mm) REVERT: H 425 MET cc_start: 0.8617 (mtt) cc_final: 0.8403 (mtt) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.6191 time to fit residues: 536.4430 Evaluate side-chains 402 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 10.0000 chunk 445 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 chunk 178 optimal weight: 0.0060 chunk 280 optimal weight: 0.7980 chunk 343 optimal weight: 5.9990 chunk 533 optimal weight: 5.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 276 GLN A 512 ASN A 549 HIS B 721 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 ASN D 292 HIS D 597 ASN ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 614 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 49075 Z= 0.139 Angle : 0.483 10.040 66451 Z= 0.258 Chirality : 0.038 0.156 7505 Planarity : 0.003 0.053 8334 Dihedral : 9.550 85.221 7287 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.54 % Allowed : 6.14 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5799 helix: 1.38 (0.09), residues: 3118 sheet: 1.01 (0.40), residues: 212 loop : -1.00 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 738 HIS 0.006 0.001 HIS D 118 PHE 0.015 0.001 PHE C 817 TYR 0.025 0.001 TYR D 146 ARG 0.010 0.000 ARG E 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 469 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: B 529 GLU cc_start: 0.7236 (mp0) cc_final: 0.6894 (mp0) REVERT: B 775 MET cc_start: 0.8287 (mmm) cc_final: 0.7943 (tpt) REVERT: C 132 MET cc_start: 0.8655 (tmm) cc_final: 0.8189 (tpp) REVERT: C 436 TYR cc_start: 0.8319 (p90) cc_final: 0.7265 (p90) outliers start: 28 outliers final: 16 residues processed: 487 average time/residue: 0.5729 time to fit residues: 461.8330 Evaluate side-chains 420 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 403 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 444 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 534 optimal weight: 10.0000 chunk 577 optimal weight: 4.9990 chunk 476 optimal weight: 8.9990 chunk 530 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 429 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN C 369 ASN D 744 ASN E 530 GLN G 560 ASN ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 751 GLN H 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 49075 Z= 0.336 Angle : 0.545 8.391 66451 Z= 0.287 Chirality : 0.041 0.162 7505 Planarity : 0.004 0.052 8334 Dihedral : 9.495 83.467 7285 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 1.27 % Allowed : 9.88 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 5799 helix: 1.36 (0.09), residues: 3147 sheet: 0.44 (0.38), residues: 231 loop : -1.13 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 738 HIS 0.007 0.001 HIS H 839 PHE 0.020 0.002 PHE C 227 TYR 0.024 0.001 TYR D 146 ARG 0.009 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 403 time to evaluate : 5.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 ASP cc_start: 0.7942 (p0) cc_final: 0.7739 (p0) REVERT: B 708 ASP cc_start: 0.8117 (p0) cc_final: 0.7909 (p0) REVERT: B 775 MET cc_start: 0.8429 (mmm) cc_final: 0.8091 (tpt) REVERT: C 132 MET cc_start: 0.8663 (tmm) cc_final: 0.8165 (tpp) REVERT: C 198 GLU cc_start: 0.8193 (tp30) cc_final: 0.7962 (tp30) REVERT: C 436 TYR cc_start: 0.8394 (p90) cc_final: 0.7019 (p90) REVERT: D 105 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7547 (mtmt) REVERT: H 75 ASP cc_start: 0.8494 (t0) cc_final: 0.8277 (t0) outliers start: 66 outliers final: 51 residues processed: 445 average time/residue: 0.5873 time to fit residues: 433.5600 Evaluate side-chains 426 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 375 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 THR Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 2.9990 chunk 402 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 536 optimal weight: 1.9990 chunk 568 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 508 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49075 Z= 0.190 Angle : 0.466 8.281 66451 Z= 0.248 Chirality : 0.038 0.151 7505 Planarity : 0.003 0.050 8334 Dihedral : 9.358 85.252 7285 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.31 % Allowed : 11.57 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5799 helix: 1.51 (0.09), residues: 3145 sheet: 0.72 (0.39), residues: 209 loop : -1.09 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 738 HIS 0.007 0.001 HIS H 392 PHE 0.016 0.001 PHE E 177 TYR 0.020 0.001 TYR D 146 ARG 0.005 0.000 ARG D 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 414 time to evaluate : 5.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (ttm) REVERT: A 426 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9218 (tt) REVERT: B 708 ASP cc_start: 0.8043 (p0) cc_final: 0.7831 (p0) REVERT: B 775 MET cc_start: 0.8402 (mmm) cc_final: 0.8098 (tpt) REVERT: C 132 MET cc_start: 0.8662 (tmm) cc_final: 0.8157 (tpp) REVERT: C 436 TYR cc_start: 0.8398 (p90) cc_final: 0.7100 (p90) REVERT: D 105 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7594 (mtmt) REVERT: D 543 ARG cc_start: 0.7417 (mmm160) cc_final: 0.7037 (mmm-85) REVERT: E 140 TYR cc_start: 0.5000 (OUTLIER) cc_final: 0.4410 (m-10) REVERT: E 744 ASN cc_start: 0.8864 (t0) cc_final: 0.8384 (t0) REVERT: H 75 ASP cc_start: 0.8469 (t0) cc_final: 0.8220 (t0) REVERT: H 431 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7474 (ptm160) REVERT: H 488 GLU cc_start: 0.7928 (tp30) cc_final: 0.7644 (tp30) REVERT: H 530 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7498 (tm-30) outliers start: 68 outliers final: 39 residues processed: 456 average time/residue: 0.5997 time to fit residues: 451.1291 Evaluate side-chains 435 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 392 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 10.0000 chunk 322 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 423 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 510 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN D 292 HIS E 530 GLN E 615 ASN ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 49075 Z= 0.450 Angle : 0.612 9.570 66451 Z= 0.321 Chirality : 0.043 0.210 7505 Planarity : 0.004 0.049 8334 Dihedral : 9.527 86.115 7285 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 2.16 % Allowed : 13.09 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 5799 helix: 1.17 (0.09), residues: 3142 sheet: 0.09 (0.37), residues: 243 loop : -1.29 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 738 HIS 0.015 0.001 HIS H 392 PHE 0.023 0.002 PHE C 227 TYR 0.023 0.002 TYR D 146 ARG 0.005 0.001 ARG E 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 390 time to evaluate : 5.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 708 ASP cc_start: 0.8215 (p0) cc_final: 0.8009 (p0) REVERT: B 775 MET cc_start: 0.8573 (mmm) cc_final: 0.8050 (tpt) REVERT: C 129 LEU cc_start: 0.9018 (tt) cc_final: 0.8733 (tt) REVERT: C 132 MET cc_start: 0.8613 (tmm) cc_final: 0.8173 (tpp) REVERT: C 443 MET cc_start: 0.8649 (tpp) cc_final: 0.8398 (mmm) REVERT: D 146 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.6004 (t80) REVERT: D 285 GLU cc_start: 0.7800 (tp30) cc_final: 0.7304 (tp30) REVERT: E 140 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.4477 (m-10) REVERT: H 75 ASP cc_start: 0.8571 (t0) cc_final: 0.8259 (t0) REVERT: H 530 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7535 (tm-30) outliers start: 112 outliers final: 77 residues processed: 473 average time/residue: 0.5961 time to fit residues: 467.2500 Evaluate side-chains 448 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 368 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 775 MET Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 THR Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 0.9980 chunk 511 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 333 optimal weight: 0.2980 chunk 140 optimal weight: 0.8980 chunk 568 optimal weight: 10.0000 chunk 472 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN G 439 HIS ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 49075 Z= 0.172 Angle : 0.471 8.794 66451 Z= 0.250 Chirality : 0.038 0.217 7505 Planarity : 0.003 0.048 8334 Dihedral : 9.314 88.591 7285 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 1.48 % Allowed : 14.83 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5799 helix: 1.48 (0.09), residues: 3141 sheet: 0.46 (0.39), residues: 209 loop : -1.16 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 738 HIS 0.005 0.001 HIS A 165 PHE 0.015 0.001 PHE E 177 TYR 0.023 0.001 TYR H 140 ARG 0.005 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 416 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7674 (ttm) REVERT: B 525 ARG cc_start: 0.8169 (tpp-160) cc_final: 0.7873 (tpp-160) REVERT: B 775 MET cc_start: 0.8409 (mmm) cc_final: 0.7936 (tpt) REVERT: C 132 MET cc_start: 0.8591 (tmm) cc_final: 0.8154 (tpp) REVERT: E 140 TYR cc_start: 0.5059 (OUTLIER) cc_final: 0.4490 (m-10) REVERT: E 744 ASN cc_start: 0.8804 (t0) cc_final: 0.8276 (t0) REVERT: H 75 ASP cc_start: 0.8549 (t0) cc_final: 0.8175 (t0) REVERT: H 488 GLU cc_start: 0.7921 (tp30) cc_final: 0.7684 (tp30) REVERT: H 530 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7569 (tm-30) outliers start: 77 outliers final: 52 residues processed: 465 average time/residue: 0.6187 time to fit residues: 475.1501 Evaluate side-chains 443 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 388 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 415 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 478 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 566 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 345 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 49075 Z= 0.340 Angle : 0.548 12.140 66451 Z= 0.287 Chirality : 0.040 0.174 7505 Planarity : 0.004 0.049 8334 Dihedral : 9.353 87.554 7285 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 1.93 % Allowed : 15.33 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 5799 helix: 1.35 (0.09), residues: 3148 sheet: 0.03 (0.37), residues: 233 loop : -1.26 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 738 HIS 0.020 0.001 HIS H 392 PHE 0.018 0.001 PHE C 227 TYR 0.021 0.001 TYR A 430 ARG 0.008 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 384 time to evaluate : 5.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8028 (t) REVERT: A 132 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7722 (ttm) REVERT: B 385 ASP cc_start: 0.8768 (t0) cc_final: 0.8450 (t0) REVERT: B 775 MET cc_start: 0.8495 (mmm) cc_final: 0.8005 (tpt) REVERT: C 129 LEU cc_start: 0.8996 (tt) cc_final: 0.8722 (tt) REVERT: C 132 MET cc_start: 0.8610 (tmm) cc_final: 0.8153 (tpp) REVERT: D 543 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7096 (mmm-85) REVERT: E 140 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4619 (m-10) REVERT: H 75 ASP cc_start: 0.8629 (t0) cc_final: 0.8310 (t0) REVERT: H 294 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: H 488 GLU cc_start: 0.7980 (tp30) cc_final: 0.7666 (tp30) REVERT: H 530 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7589 (tm-30) outliers start: 100 outliers final: 80 residues processed: 452 average time/residue: 0.5883 time to fit residues: 445.8827 Evaluate side-chains 457 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 372 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain C residue 928 ASP Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 775 MET Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 931 THR Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 0.0370 chunk 226 optimal weight: 20.0000 chunk 338 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 111 optimal weight: 0.0970 chunk 109 optimal weight: 0.7980 chunk 360 optimal weight: 4.9990 chunk 386 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 49075 Z= 0.129 Angle : 0.456 11.376 66451 Z= 0.241 Chirality : 0.037 0.165 7505 Planarity : 0.003 0.049 8334 Dihedral : 9.143 89.739 7285 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 1.25 % Allowed : 16.45 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5799 helix: 1.61 (0.09), residues: 3149 sheet: 0.55 (0.40), residues: 208 loop : -1.12 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 738 HIS 0.028 0.001 HIS H 392 PHE 0.015 0.001 PHE H 528 TYR 0.020 0.001 TYR H 140 ARG 0.005 0.000 ARG D 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 420 time to evaluate : 5.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7650 (ttm) REVERT: B 385 ASP cc_start: 0.8660 (t0) cc_final: 0.8417 (t70) REVERT: B 525 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7863 (tpp-160) REVERT: B 775 MET cc_start: 0.8359 (mmm) cc_final: 0.7889 (tpt) REVERT: C 47 ASN cc_start: 0.7864 (m110) cc_final: 0.7659 (m110) REVERT: C 132 MET cc_start: 0.8641 (tmm) cc_final: 0.8203 (tpp) REVERT: D 543 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7141 (mmm-85) REVERT: E 140 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.4609 (m-10) REVERT: E 275 GLU cc_start: 0.7867 (pp20) cc_final: 0.7633 (pp20) REVERT: E 744 ASN cc_start: 0.8761 (t0) cc_final: 0.8343 (t0) REVERT: H 75 ASP cc_start: 0.8561 (t0) cc_final: 0.8225 (t0) REVERT: H 530 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7583 (tm-30) outliers start: 65 outliers final: 46 residues processed: 466 average time/residue: 0.5901 time to fit residues: 454.9840 Evaluate side-chains 433 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 384 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 931 THR Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 788 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 7.9990 chunk 542 optimal weight: 9.9990 chunk 495 optimal weight: 4.9990 chunk 528 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 414 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 477 optimal weight: 10.0000 chunk 499 optimal weight: 9.9990 chunk 526 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN B 597 ASN B 614 ASN D 103 ASN E 530 GLN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 49075 Z= 0.374 Angle : 0.570 12.675 66451 Z= 0.297 Chirality : 0.041 0.162 7505 Planarity : 0.004 0.050 8334 Dihedral : 9.256 88.864 7285 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 1.69 % Allowed : 16.31 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5799 helix: 1.39 (0.09), residues: 3157 sheet: 0.11 (0.38), residues: 234 loop : -1.25 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 738 HIS 0.006 0.001 HIS A 165 PHE 0.019 0.002 PHE C 227 TYR 0.027 0.002 TYR H 140 ARG 0.011 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 377 time to evaluate : 5.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7756 (ttm) REVERT: B 525 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7698 (tpp-160) REVERT: B 775 MET cc_start: 0.8567 (mmm) cc_final: 0.8109 (tpt) REVERT: C 129 LEU cc_start: 0.9018 (tt) cc_final: 0.8752 (tt) REVERT: C 132 MET cc_start: 0.8573 (tmm) cc_final: 0.8145 (tpp) REVERT: D 543 ARG cc_start: 0.7584 (mmm160) cc_final: 0.7233 (mmm-85) REVERT: E 140 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.4786 (m-10) REVERT: E 275 GLU cc_start: 0.7815 (pp20) cc_final: 0.7599 (pp20) REVERT: H 75 ASP cc_start: 0.8669 (t0) cc_final: 0.8354 (t0) REVERT: H 530 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7617 (tm-30) outliers start: 88 outliers final: 71 residues processed: 439 average time/residue: 0.6096 time to fit residues: 443.7107 Evaluate side-chains 447 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 373 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 931 THR Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 20.0000 chunk 558 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 585 optimal weight: 10.0000 chunk 539 optimal weight: 6.9990 chunk 466 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 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 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 HIS A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN E 530 GLN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 49075 Z= 0.342 Angle : 0.558 12.457 66451 Z= 0.292 Chirality : 0.041 0.164 7505 Planarity : 0.004 0.050 8334 Dihedral : 9.291 87.773 7285 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 1.66 % Allowed : 16.48 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 5799 helix: 1.33 (0.09), residues: 3149 sheet: 0.02 (0.36), residues: 244 loop : -1.30 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 738 HIS 0.016 0.001 HIS H 392 PHE 0.018 0.001 PHE C 227 TYR 0.029 0.001 TYR H 140 ARG 0.005 0.000 ARG D 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 377 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: B 525 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7736 (tpp-160) REVERT: B 529 GLU cc_start: 0.7561 (pm20) cc_final: 0.7337 (mp0) REVERT: B 539 MET cc_start: 0.8562 (tpp) cc_final: 0.8320 (ttm) REVERT: B 775 MET cc_start: 0.8515 (mmm) cc_final: 0.8035 (tpt) REVERT: C 129 LEU cc_start: 0.8999 (tt) cc_final: 0.8746 (tt) REVERT: C 132 MET cc_start: 0.8563 (tmm) cc_final: 0.8111 (tpp) REVERT: D 775 MET cc_start: 0.8376 (mmm) cc_final: 0.7998 (mmp) REVERT: E 140 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.4736 (m-10) REVERT: H 75 ASP cc_start: 0.8680 (t0) cc_final: 0.8376 (t0) REVERT: H 530 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: H 818 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7974 (tm-30) outliers start: 86 outliers final: 71 residues processed: 437 average time/residue: 0.6425 time to fit residues: 468.6738 Evaluate side-chains 442 residues out of total 5193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 368 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 CYS Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 931 THR Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 350 ASP Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 615 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 788 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 0.9980 chunk 496 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 467 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 479 optimal weight: 0.2980 chunk 59 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088807 restraints weight = 97293.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091084 restraints weight = 60662.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092651 restraints weight = 44701.617| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 49075 Z= 0.159 Angle : 0.480 12.431 66451 Z= 0.252 Chirality : 0.038 0.162 7505 Planarity : 0.003 0.049 8334 Dihedral : 9.126 88.840 7285 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 1.35 % Allowed : 16.93 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5799 helix: 1.56 (0.09), residues: 3153 sheet: 0.40 (0.39), residues: 209 loop : -1.15 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 738 HIS 0.028 0.001 HIS H 392 PHE 0.015 0.001 PHE H 528 TYR 0.027 0.001 TYR H 391 ARG 0.008 0.000 ARG D 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9189.74 seconds wall clock time: 167 minutes 37.69 seconds (10057.69 seconds total)