Starting phenix.real_space_refine on Fri May 17 04:02:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/05_2024/8wyb_37922_neut_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 8 5.49 5 S 132 5.16 5 C 23014 2.51 5 N 5724 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 746": "OE1" <-> "OE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 693": "OE1" <-> "OE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D GLU 986": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 35604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7940 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7948 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "C" Number of atoms: 7915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7915 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 18, 'TRANS': 929} Chain breaks: 7 Chain: "D" Number of atoms: 7921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7921 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 19, 'TRANS': 929} Chain breaks: 7 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "F" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.96, per 1000 atoms: 0.50 Number of scatterers: 35604 At special positions: 0 Unit cell: (100.067, 130.666, 258.851, 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 132 16.00 P 8 15.00 O 6726 8.00 N 5724 7.00 C 23014 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: 14.24 Conformation dependent library (CDL) restraints added in 6.0 seconds 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 233 helices and 15 sheets defined 54.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.30 Creating SS restraints... Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.806A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 71 Processing helix chain 'A' and resid 81 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.603A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.807A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.668A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 Proline residue: A 318 - end of helix removed outlier: 5.049A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.648A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.717A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 4.626A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 552 through 571 Processing helix chain 'A' and resid 580 through 597 Processing helix chain 'A' and resid 601 through 604 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 706 through 724 removed outlier: 3.819A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 751 through 764 removed outlier: 4.178A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 801 through 812 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 832 through 840 removed outlier: 3.904A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 847 through 856 removed outlier: 3.581A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 879 through 896 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 941 through 944 No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 946 through 948 No H-bonds generated for 'chain 'A' and resid 946 through 948' Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 956 through 961 removed outlier: 3.557A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 995 through 1002 Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.756A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 81 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.718A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.995A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.618A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.534A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Proline residue: B 318 - end of helix removed outlier: 4.663A pdb=" N ALA B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 333 removed outlier: 4.117A pdb=" N LYS B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.612A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 432 through 444 Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 469 through 500 removed outlier: 4.679A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 552 through 571 Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.550A pdb=" N GLU B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 604 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 619 through 627 Processing helix chain 'B' and resid 649 through 658 Processing helix chain 'B' and resid 661 through 670 Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 706 through 725 removed outlier: 4.731A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 725 " --> pdb=" O TYR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 741 Processing helix chain 'B' and resid 751 through 764 removed outlier: 3.761A pdb=" N LYS B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 785 Processing helix chain 'B' and resid 801 through 812 Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 847 through 856 removed outlier: 3.986A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 879 through 896 Processing helix chain 'B' and resid 912 through 921 Processing helix chain 'B' and resid 930 through 933 Processing helix chain 'B' and resid 941 through 944 No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 964 through 973 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 995 through 1003 removed outlier: 3.674A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 38 Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.406A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 81 through 107 removed outlier: 4.019A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 7.152A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 3.541A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 156 through 159 No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 223 through 234 removed outlier: 4.133A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 307 through 321 Proline residue: C 318 - end of helix removed outlier: 4.932A pdb=" N ALA C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 356 through 364 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 432 through 444 removed outlier: 3.785A pdb=" N LYS C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 removed outlier: 4.475A pdb=" N ILE C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 509 through 518 Processing helix chain 'C' and resid 524 through 527 No H-bonds generated for 'chain 'C' and resid 524 through 527' Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.375A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 571 Processing helix chain 'C' and resid 580 through 597 Processing helix chain 'C' and resid 601 through 604 Processing helix chain 'C' and resid 606 through 615 Processing helix chain 'C' and resid 619 through 627 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 661 through 670 Processing helix chain 'C' and resid 681 through 699 Processing helix chain 'C' and resid 706 through 724 removed outlier: 3.914A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS C 724 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 741 Processing helix chain 'C' and resid 751 through 764 removed outlier: 4.281A pdb=" N CYS C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 785 Processing helix chain 'C' and resid 801 through 812 removed outlier: 3.577A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 Processing helix chain 'C' and resid 832 through 840 removed outlier: 3.802A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 847 through 856 removed outlier: 4.279A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 871 Processing helix chain 'C' and resid 879 through 896 Processing helix chain 'C' and resid 912 through 921 Processing helix chain 'C' and resid 930 through 933 Processing helix chain 'C' and resid 941 through 944 No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 946 through 948 No H-bonds generated for 'chain 'C' and resid 946 through 948' Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 956 through 961 removed outlier: 3.538A pdb=" N LYS C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 977 through 990 Processing helix chain 'C' and resid 995 through 1003 Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 81 through 94 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.523A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 193 through 196 No H-bonds generated for 'chain 'D' and resid 193 through 196' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 283 through 294 removed outlier: 3.712A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 Processing helix chain 'D' and resid 318 through 321 removed outlier: 3.552A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.575A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 364 Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 375 through 391 removed outlier: 3.750A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 469 through 494 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 526 through 529 No H-bonds generated for 'chain 'D' and resid 526 through 529' Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 541 through 546 removed outlier: 4.084A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 571 Processing helix chain 'D' and resid 580 through 595 Processing helix chain 'D' and resid 601 through 604 Processing helix chain 'D' and resid 606 through 615 Processing helix chain 'D' and resid 619 through 627 Processing helix chain 'D' and resid 649 through 658 Processing helix chain 'D' and resid 661 through 670 Processing helix chain 'D' and resid 681 through 700 Processing helix chain 'D' and resid 706 through 725 removed outlier: 3.578A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 741 Processing helix chain 'D' and resid 751 through 764 removed outlier: 4.424A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 785 Processing helix chain 'D' and resid 801 through 812 Processing helix chain 'D' and resid 818 through 826 Processing helix chain 'D' and resid 832 through 838 Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 847 through 856 removed outlier: 4.019A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 871 Processing helix chain 'D' and resid 879 through 896 Processing helix chain 'D' and resid 913 through 921 Processing helix chain 'D' and resid 930 through 933 Processing helix chain 'D' and resid 941 through 944 No H-bonds generated for 'chain 'D' and resid 941 through 944' Processing helix chain 'D' and resid 946 through 948 No H-bonds generated for 'chain 'D' and resid 946 through 948' Processing helix chain 'D' and resid 951 through 953 No H-bonds generated for 'chain 'D' and resid 951 through 953' Processing helix chain 'D' and resid 956 through 960 Processing helix chain 'D' and resid 964 through 973 Processing helix chain 'D' and resid 977 through 990 Processing helix chain 'D' and resid 995 through 1002 Processing helix chain 'E' and resid 70 through 76 Processing helix chain 'F' and resid 70 through 76 Processing helix chain 'G' and resid 70 through 76 Processing helix chain 'H' and resid 70 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.473A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR A 212 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE A 45 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 214 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 244 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= C, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.520A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR B 212 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 45 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL B 214 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 244 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= E, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.869A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR C 212 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE C 45 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL C 214 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE C 244 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG C 267 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG C 247 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 269 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 150 through 152 Processing sheet with id= G, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= H, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.393A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR D 212 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 45 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL D 214 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 244 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= J, first strand: chain 'E' and resid 233 through 235 removed outlier: 3.809A pdb=" N ASP E 10 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG E 15 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 21 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 198 through 200 removed outlier: 4.869A pdb=" N ILE E 59 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 29 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 193 through 196 removed outlier: 4.017A pdb=" N ASP F 10 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG F 15 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU F 21 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE F 32 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN F 34 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 56 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE F 59 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS F 219 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 233 through 235 removed outlier: 3.769A pdb=" N ASP G 10 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 23 " --> pdb=" O PHE G 13 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG G 15 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 21 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 198 through 200 removed outlier: 5.342A pdb=" N ILE G 59 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 29 " --> pdb=" O THR G 62 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 233 through 235 removed outlier: 3.538A pdb=" N ASP H 10 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG H 15 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU H 21 " --> pdb=" O ARG H 15 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR H 62 " --> pdb=" O GLN H 28 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA H 30 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN H 60 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE H 32 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU H 58 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN H 34 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU H 56 " --> pdb=" O GLN H 34 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE H 59 " --> pdb=" O ALA H 222 " (cutoff:3.500A) 1502 hydrogen bonds defined for protein. 4374 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: 14.56 Time building geometry restraints manager: 15.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5990 1.32 - 1.44: 10180 1.44 - 1.57: 19991 1.57 - 1.69: 8 1.69 - 1.82: 228 Bond restraints: 36397 Sorted by residual: bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.503 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3 NAD D1101 " pdb=" PN NAD D1101 " ideal model delta sigma weight residual 1.633 1.501 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" O3 NAD D1101 " pdb=" PA NAD D1101 " ideal model delta sigma weight residual 1.653 1.541 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O3 NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 36392 not shown) Histogram of bond angle deviations from ideal: 81.78 - 92.89: 5 92.89 - 104.01: 339 104.01 - 115.12: 21362 115.12 - 126.23: 26963 126.23 - 137.34: 364 Bond angle restraints: 49033 Sorted by residual: angle pdb=" CA PRO A 956 " pdb=" N PRO A 956 " pdb=" CD PRO A 956 " ideal model delta sigma weight residual 112.00 96.44 15.56 1.40e+00 5.10e-01 1.24e+02 angle pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" O2B NAD B1101 " ideal model delta sigma weight residual 113.98 84.70 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" O2B NAD A1101 " ideal model delta sigma weight residual 113.98 84.71 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C1B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" O2B NAD C1101 " ideal model delta sigma weight residual 113.98 89.98 24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" CA PRO B 57 " pdb=" N PRO B 57 " pdb=" CD PRO B 57 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 ... (remaining 49028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 18606 20.13 - 40.26: 2558 40.26 - 60.38: 517 60.38 - 80.51: 91 80.51 - 100.64: 35 Dihedral angle restraints: 21807 sinusoidal: 9188 harmonic: 12619 Sorted by residual: dihedral pdb=" CA HIS C 349 " pdb=" C HIS C 349 " pdb=" N LYS C 350 " pdb=" CA LYS C 350 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA SER A 615 " pdb=" C SER A 615 " pdb=" N MET A 616 " pdb=" CA MET A 616 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU E 208 " pdb=" C LEU E 208 " pdb=" N GLU E 209 " pdb=" CA GLU E 209 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 21804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4910 0.084 - 0.167: 299 0.167 - 0.251: 20 0.251 - 0.335: 4 0.335 - 0.418: 2 Chirality restraints: 5235 Sorted by residual: chirality pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" N9A NAD A1101 " pdb=" O4B NAD A1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" N9A NAD B1101 " pdb=" O4B NAD B1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" C4B NAD C1101 " pdb=" O3B NAD C1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 5232 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 955 " 0.106 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO A 956 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 956 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 956 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 56 " 0.076 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 57 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 381 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 381 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 381 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 381 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 386 2.59 - 3.17: 31339 3.17 - 3.75: 58676 3.75 - 4.32: 80901 4.32 - 4.90: 132890 Nonbonded interactions: 304192 Sorted by model distance: nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 2.015 2.440 nonbonded pdb=" OD1 ASN A 78 " pdb=" N TYR A 79 " model vdw 2.068 2.520 nonbonded pdb=" OH TYR A 589 " pdb=" OD1 ASP A 651 " model vdw 2.103 2.440 nonbonded pdb=" OH TYR B 800 " pdb=" O ALA E 224 " model vdw 2.119 2.440 nonbonded pdb=" NZ LYS F 16 " pdb=" OD1 ASN F 197 " model vdw 2.158 2.520 ... (remaining 304187 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 23 through 72 or resid 79 through 463 or resid 467 through \ 633 or resid 644 through 1005 or resid 1101)) selection = (chain 'B' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1005 or resid 1101)) selection = (chain 'C' and (resid 23 through 296 or resid 304 through 463 or resid 467 throu \ gh 633 or resid 644 through 1005 or resid 1101)) selection = (chain 'D' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1005 or resid 1101)) } ncs_group { reference = (chain 'E' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'F' and (resid 8 through 176 or resid 191 through 236)) selection = (chain 'G' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'H' and (resid 8 through 176 or resid 191 through 236)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 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: 21.470 Check model and map are aligned: 0.280 Set scattering table: 0.310 Process input model: 95.340 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.005 0.159 36397 Z= 0.286 Angle : 0.818 29.279 49033 Z= 0.406 Chirality : 0.044 0.418 5235 Planarity : 0.004 0.147 6216 Dihedral : 18.623 100.641 13667 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.51 % Allowed : 29.35 % Favored : 70.13 % 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: -0.12 (0.13), residues: 4155 helix: 0.61 (0.11), residues: 2423 sheet: -0.27 (0.34), residues: 190 loop : -1.07 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 919 HIS 0.007 0.001 HIS C 349 PHE 0.055 0.002 PHE C 381 TYR 0.048 0.002 TYR B 282 ARG 0.011 0.001 ARG C 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 414 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.7831 (t80) cc_final: 0.7499 (t80) REVERT: D 330 LEU cc_start: 0.8290 (tp) cc_final: 0.8085 (tt) REVERT: E 194 GLN cc_start: 0.5819 (tm-30) cc_final: 0.5587 (mp10) outliers start: 20 outliers final: 11 residues processed: 426 average time/residue: 0.4900 time to fit residues: 346.5260 Evaluate side-chains 394 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 383 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1003 TYR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain F residue 32 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 356 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 170 optimal weight: 0.4980 chunk 330 optimal weight: 30.0000 chunk 127 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 246 optimal weight: 5.9990 chunk 383 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 487 GLN A 698 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 58 GLN C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 491 GLN D 521 ASN D 549 GLN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36397 Z= 0.184 Angle : 0.545 9.430 49033 Z= 0.281 Chirality : 0.040 0.209 5235 Planarity : 0.004 0.079 6216 Dihedral : 8.437 87.609 4895 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.08 % Allowed : 26.84 % Favored : 71.08 % 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: 0.06 (0.13), residues: 4155 helix: 0.78 (0.11), residues: 2442 sheet: -0.29 (0.33), residues: 214 loop : -1.05 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 601 HIS 0.008 0.001 HIS C 658 PHE 0.024 0.001 PHE C 381 TYR 0.042 0.001 TYR D 418 ARG 0.008 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 426 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.7978 (t80) cc_final: 0.7772 (t80) REVERT: B 134 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6777 (p90) REVERT: C 274 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 674 ASP cc_start: 0.6484 (m-30) cc_final: 0.6218 (p0) REVERT: C 693 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: D 280 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7483 (t80) REVERT: D 330 LEU cc_start: 0.8399 (tp) cc_final: 0.8192 (tt) REVERT: H 32 PHE cc_start: 0.3033 (OUTLIER) cc_final: 0.2676 (m-80) outliers start: 81 outliers final: 21 residues processed: 489 average time/residue: 0.4933 time to fit residues: 393.6790 Evaluate side-chains 413 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 387 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 383 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36397 Z= 0.300 Angle : 0.574 10.708 49033 Z= 0.299 Chirality : 0.042 0.203 5235 Planarity : 0.004 0.059 6216 Dihedral : 7.166 84.882 4881 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.18 % Allowed : 26.27 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4155 helix: 0.76 (0.10), residues: 2431 sheet: -0.44 (0.33), residues: 224 loop : -1.12 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 72 HIS 0.008 0.001 HIS A 609 PHE 0.019 0.002 PHE B 699 TYR 0.026 0.002 TYR B 755 ARG 0.005 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 414 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6743 (p90) REVERT: B 448 TRP cc_start: 0.8875 (m-10) cc_final: 0.8409 (m-10) REVERT: B 610 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: B 862 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6935 (mt) REVERT: C 421 MET cc_start: 0.5297 (ptp) cc_final: 0.5051 (ptp) REVERT: C 693 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: D 107 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6735 (t80) REVERT: D 144 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8242 (mtmm) REVERT: D 280 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 511 PHE cc_start: 0.4515 (OUTLIER) cc_final: 0.4277 (m-80) REVERT: E 62 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7716 (t) REVERT: G 50 LEU cc_start: -0.0571 (OUTLIER) cc_final: -0.0838 (mm) REVERT: H 32 PHE cc_start: 0.2686 (OUTLIER) cc_final: 0.2114 (m-80) REVERT: H 75 MET cc_start: 0.3348 (mmp) cc_final: 0.1034 (ptp) outliers start: 124 outliers final: 55 residues processed: 507 average time/residue: 0.4680 time to fit residues: 397.8295 Evaluate side-chains 449 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 383 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 356 TYR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 379 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 183 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 385 optimal weight: 2.9990 chunk 407 optimal weight: 9.9990 chunk 201 optimal weight: 0.0570 chunk 365 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 698 GLN A 834 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36397 Z= 0.203 Angle : 0.529 11.693 49033 Z= 0.274 Chirality : 0.039 0.171 5235 Planarity : 0.003 0.049 6216 Dihedral : 6.728 77.002 4881 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.13 % Allowed : 26.61 % Favored : 70.26 % 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: 0.07 (0.13), residues: 4155 helix: 0.83 (0.11), residues: 2436 sheet: -0.34 (0.33), residues: 224 loop : -1.13 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 448 HIS 0.006 0.001 HIS C 349 PHE 0.025 0.001 PHE E 67 TYR 0.036 0.001 TYR B 755 ARG 0.005 0.000 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 413 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.9248 (tt) cc_final: 0.9045 (tp) REVERT: A 744 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8434 (t80) REVERT: A 930 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.3761 (mmm) REVERT: B 134 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6874 (p90) REVERT: B 448 TRP cc_start: 0.8825 (m-10) cc_final: 0.8473 (m-10) REVERT: B 495 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 531 MET cc_start: 0.8915 (mmp) cc_final: 0.8541 (mmt) REVERT: B 781 LEU cc_start: 0.8440 (tt) cc_final: 0.8183 (mp) REVERT: B 810 HIS cc_start: 0.7666 (t-90) cc_final: 0.7447 (t-170) REVERT: C 372 LYS cc_start: 0.4370 (pmtt) cc_final: 0.2851 (ttmt) REVERT: C 674 ASP cc_start: 0.6327 (m-30) cc_final: 0.5978 (p0) REVERT: D 107 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6810 (t80) REVERT: D 144 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: D 280 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 511 PHE cc_start: 0.4492 (OUTLIER) cc_final: 0.4254 (m-80) REVERT: G 50 LEU cc_start: -0.0628 (OUTLIER) cc_final: -0.0868 (mm) REVERT: H 32 PHE cc_start: 0.2564 (OUTLIER) cc_final: 0.1833 (m-80) REVERT: H 75 MET cc_start: 0.3395 (mmp) cc_final: 0.1393 (ptt) outliers start: 122 outliers final: 57 residues processed: 505 average time/residue: 0.4768 time to fit residues: 404.4850 Evaluate side-chains 448 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 381 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 356 TYR Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 548 ASN Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 339 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 366 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 125 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 HIS ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36397 Z= 0.241 Angle : 0.544 12.686 49033 Z= 0.281 Chirality : 0.040 0.182 5235 Planarity : 0.003 0.045 6216 Dihedral : 6.562 70.704 4881 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.26 % Allowed : 26.68 % Favored : 70.06 % 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: 0.12 (0.13), residues: 4155 helix: 0.86 (0.11), residues: 2427 sheet: -0.21 (0.35), residues: 200 loop : -1.09 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 72 HIS 0.006 0.001 HIS C 658 PHE 0.023 0.001 PHE B 699 TYR 0.034 0.001 TYR B 755 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 405 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7033 (mt0) REVERT: A 721 TYR cc_start: 0.8703 (t80) cc_final: 0.7827 (t80) REVERT: A 744 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8488 (t80) REVERT: A 930 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3851 (mmm) REVERT: B 395 CYS cc_start: 0.8191 (p) cc_final: 0.7434 (t) REVERT: B 448 TRP cc_start: 0.8861 (m-10) cc_final: 0.8411 (m-10) REVERT: B 495 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7721 (tp) REVERT: B 781 LEU cc_start: 0.8417 (tt) cc_final: 0.8186 (mp) REVERT: B 930 MET cc_start: 0.5783 (mmt) cc_final: 0.4904 (ptp) REVERT: C 101 ASP cc_start: 0.7747 (m-30) cc_final: 0.7494 (m-30) REVERT: C 258 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8877 (tp) REVERT: C 372 LYS cc_start: 0.4494 (pmtt) cc_final: 0.2908 (ttmt) REVERT: C 674 ASP cc_start: 0.6336 (m-30) cc_final: 0.6131 (p0) REVERT: C 693 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: D 107 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6796 (t80) REVERT: D 144 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: D 280 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7572 (t80) REVERT: D 511 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.4395 (m-80) REVERT: E 194 GLN cc_start: 0.6115 (tm-30) cc_final: 0.5898 (mp10) REVERT: G 50 LEU cc_start: -0.0574 (OUTLIER) cc_final: -0.0807 (mm) REVERT: H 32 PHE cc_start: 0.2508 (OUTLIER) cc_final: 0.1767 (m-80) outliers start: 127 outliers final: 69 residues processed: 504 average time/residue: 0.4905 time to fit residues: 409.0572 Evaluate side-chains 456 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 375 time to evaluate : 4.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 0.9990 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 100 optimal weight: 0.0270 chunk 408 optimal weight: 20.0000 chunk 338 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 214 optimal weight: 0.0570 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36397 Z= 0.157 Angle : 0.518 10.539 49033 Z= 0.266 Chirality : 0.039 0.256 5235 Planarity : 0.003 0.042 6216 Dihedral : 6.306 63.383 4881 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.44 % Allowed : 27.22 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 4155 helix: 0.97 (0.11), residues: 2428 sheet: -0.12 (0.36), residues: 200 loop : -1.04 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 72 HIS 0.006 0.001 HIS C 658 PHE 0.031 0.001 PHE C 381 TYR 0.033 0.001 TYR B 755 ARG 0.008 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 405 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8034 (t80) cc_final: 0.7191 (t80) REVERT: A 721 TYR cc_start: 0.8678 (t80) cc_final: 0.7792 (t80) REVERT: A 744 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8541 (t80) REVERT: A 930 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.3796 (mmm) REVERT: B 270 ASP cc_start: 0.8106 (t70) cc_final: 0.7667 (t0) REVERT: B 357 MET cc_start: 0.8345 (tpp) cc_final: 0.7874 (tpt) REVERT: B 395 CYS cc_start: 0.8098 (p) cc_final: 0.7323 (t) REVERT: B 448 TRP cc_start: 0.8824 (m-10) cc_final: 0.8319 (m-10) REVERT: B 495 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7740 (tp) REVERT: B 930 MET cc_start: 0.5709 (mmt) cc_final: 0.4858 (ptp) REVERT: C 101 ASP cc_start: 0.7765 (m-30) cc_final: 0.7532 (m-30) REVERT: C 372 LYS cc_start: 0.4426 (pmtt) cc_final: 0.2924 (ttmt) REVERT: C 421 MET cc_start: 0.5510 (ptp) cc_final: 0.5232 (ptp) REVERT: C 611 TYR cc_start: 0.7292 (t80) cc_final: 0.7082 (t80) REVERT: C 693 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: D 107 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6801 (t80) REVERT: D 134 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: D 144 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8084 (mtmm) REVERT: D 280 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7521 (t80) outliers start: 95 outliers final: 59 residues processed: 471 average time/residue: 0.4741 time to fit residues: 371.9375 Evaluate side-chains 444 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 377 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 393 optimal weight: 3.9990 chunk 46 optimal weight: 0.0470 chunk 232 optimal weight: 0.2980 chunk 298 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 406 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 548 ASN D 549 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36397 Z= 0.283 Angle : 0.558 12.076 49033 Z= 0.288 Chirality : 0.041 0.172 5235 Planarity : 0.003 0.041 6216 Dihedral : 6.245 59.018 4881 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.85 % Allowed : 26.66 % Favored : 70.49 % 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 (0.13), residues: 4155 helix: 0.92 (0.11), residues: 2428 sheet: -0.37 (0.35), residues: 220 loop : -1.07 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 72 HIS 0.006 0.001 HIS C 658 PHE 0.026 0.002 PHE C 544 TYR 0.030 0.001 TYR B 755 ARG 0.007 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 386 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6675 (mt0) REVERT: A 744 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: A 930 MET cc_start: 0.4443 (OUTLIER) cc_final: 0.3914 (mmm) REVERT: B 270 ASP cc_start: 0.8202 (t70) cc_final: 0.7750 (t0) REVERT: B 287 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7548 (m) REVERT: B 395 CYS cc_start: 0.8146 (p) cc_final: 0.7413 (t) REVERT: B 448 TRP cc_start: 0.8902 (m-10) cc_final: 0.8505 (m-10) REVERT: B 495 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7726 (tp) REVERT: B 781 LEU cc_start: 0.8383 (tt) cc_final: 0.8137 (mp) REVERT: B 930 MET cc_start: 0.5802 (mmt) cc_final: 0.4941 (ptp) REVERT: C 101 ASP cc_start: 0.7812 (m-30) cc_final: 0.7607 (m-30) REVERT: C 330 LEU cc_start: 0.8036 (mt) cc_final: 0.7653 (mm) REVERT: C 372 LYS cc_start: 0.4570 (pmtt) cc_final: 0.3002 (ttmt) REVERT: C 421 MET cc_start: 0.5453 (ptp) cc_final: 0.5223 (ptp) REVERT: C 445 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8098 (pp) REVERT: C 611 TYR cc_start: 0.7353 (t80) cc_final: 0.7122 (t80) REVERT: C 693 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: D 107 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6812 (t80) REVERT: D 134 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: D 144 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8270 (mtmm) REVERT: D 280 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7568 (t80) outliers start: 111 outliers final: 78 residues processed: 468 average time/residue: 0.4646 time to fit residues: 362.8303 Evaluate side-chains 456 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 367 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 251 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 0.0070 chunk 258 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36397 Z= 0.249 Angle : 0.556 13.896 49033 Z= 0.285 Chirality : 0.040 0.209 5235 Planarity : 0.003 0.040 6216 Dihedral : 6.122 58.830 4881 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 27.12 % Favored : 70.18 % 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: 0.17 (0.13), residues: 4155 helix: 0.91 (0.11), residues: 2414 sheet: -0.42 (0.35), residues: 220 loop : -1.04 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 601 HIS 0.005 0.001 HIS C 658 PHE 0.022 0.002 PHE C 544 TYR 0.025 0.001 TYR B 755 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 396 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8176 (t80) cc_final: 0.7658 (t80) REVERT: A 744 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: A 930 MET cc_start: 0.4482 (OUTLIER) cc_final: 0.3960 (mmm) REVERT: B 270 ASP cc_start: 0.8175 (t70) cc_final: 0.7732 (t0) REVERT: B 287 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7535 (m) REVERT: B 395 CYS cc_start: 0.8098 (p) cc_final: 0.7399 (t) REVERT: B 448 TRP cc_start: 0.8898 (m-10) cc_final: 0.8501 (m-10) REVERT: B 495 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 781 LEU cc_start: 0.8382 (tt) cc_final: 0.8143 (mp) REVERT: B 930 MET cc_start: 0.5841 (mmt) cc_final: 0.4934 (ptp) REVERT: C 330 LEU cc_start: 0.8065 (mt) cc_final: 0.7683 (mm) REVERT: C 372 LYS cc_start: 0.4654 (pmtt) cc_final: 0.2997 (ttmt) REVERT: C 421 MET cc_start: 0.5428 (ptp) cc_final: 0.5213 (ptp) REVERT: C 445 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 611 TYR cc_start: 0.7393 (t80) cc_final: 0.7147 (t80) REVERT: C 693 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: D 107 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6829 (t80) REVERT: D 134 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: D 144 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: D 280 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7621 (t80) REVERT: D 396 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.2132 (mmt) REVERT: D 421 MET cc_start: 0.5396 (mmt) cc_final: 0.5003 (mmt) outliers start: 105 outliers final: 79 residues processed: 472 average time/residue: 0.4655 time to fit residues: 369.0406 Evaluate side-chains 462 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 372 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 369 optimal weight: 30.0000 chunk 389 optimal weight: 0.7980 chunk 355 optimal weight: 20.0000 chunk 379 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 342 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 377 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 832 GLN ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36397 Z= 0.334 Angle : 0.607 15.575 49033 Z= 0.313 Chirality : 0.042 0.178 5235 Planarity : 0.003 0.047 6216 Dihedral : 6.153 59.159 4881 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.72 % Allowed : 27.32 % Favored : 69.95 % 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: 0.02 (0.13), residues: 4155 helix: 0.76 (0.11), residues: 2410 sheet: -0.35 (0.35), residues: 214 loop : -1.05 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 72 HIS 0.007 0.001 HIS D 609 PHE 0.024 0.002 PHE A 942 TYR 0.027 0.002 TYR B 755 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 381 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7561 (m) REVERT: B 395 CYS cc_start: 0.8152 (p) cc_final: 0.7483 (t) REVERT: B 448 TRP cc_start: 0.8918 (m-10) cc_final: 0.8503 (m-10) REVERT: B 495 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 826 CYS cc_start: 0.7576 (t) cc_final: 0.7297 (t) REVERT: B 930 MET cc_start: 0.5785 (mmt) cc_final: 0.4865 (ptp) REVERT: C 372 LYS cc_start: 0.4777 (pmtt) cc_final: 0.3041 (ttmt) REVERT: C 421 MET cc_start: 0.5220 (ptp) cc_final: 0.5004 (ptp) REVERT: C 445 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (pp) REVERT: C 693 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: D 107 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6828 (t80) REVERT: D 134 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: D 144 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8317 (mtmm) REVERT: D 280 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7685 (t80) REVERT: D 421 MET cc_start: 0.5382 (mmt) cc_final: 0.4927 (mmt) REVERT: D 578 MET cc_start: 0.5687 (tmm) cc_final: 0.5444 (tpp) outliers start: 106 outliers final: 81 residues processed: 459 average time/residue: 0.4762 time to fit residues: 364.6797 Evaluate side-chains 454 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 365 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 248 optimal weight: 1.9990 chunk 400 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 420 optimal weight: 2.9990 chunk 386 optimal weight: 0.8980 chunk 334 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36397 Z= 0.320 Angle : 0.606 14.904 49033 Z= 0.310 Chirality : 0.042 0.223 5235 Planarity : 0.003 0.043 6216 Dihedral : 6.116 59.370 4881 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.52 % Allowed : 27.79 % Favored : 69.70 % 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: -0.04 (0.13), residues: 4155 helix: 0.70 (0.11), residues: 2414 sheet: -0.39 (0.35), residues: 214 loop : -1.06 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 601 HIS 0.006 0.001 HIS C 349 PHE 0.026 0.002 PHE B 815 TYR 0.028 0.002 TYR B 755 ARG 0.005 0.000 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 376 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7603 (m) REVERT: B 395 CYS cc_start: 0.8148 (p) cc_final: 0.7481 (t) REVERT: B 448 TRP cc_start: 0.8918 (m-10) cc_final: 0.8489 (m-10) REVERT: B 495 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7805 (tp) REVERT: B 826 CYS cc_start: 0.7713 (t) cc_final: 0.7433 (t) REVERT: B 941 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.5426 (m-30) REVERT: C 372 LYS cc_start: 0.4859 (pmtt) cc_final: 0.3043 (ttmt) REVERT: C 421 MET cc_start: 0.5293 (ptp) cc_final: 0.5083 (ptp) REVERT: C 611 TYR cc_start: 0.7574 (t80) cc_final: 0.7357 (t80) REVERT: C 693 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: D 107 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6829 (t80) REVERT: D 144 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8289 (mtmm) REVERT: D 280 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7719 (t80) REVERT: D 421 MET cc_start: 0.5230 (mmt) cc_final: 0.4792 (mmt) REVERT: D 578 MET cc_start: 0.5742 (tmm) cc_final: 0.5534 (tpp) REVERT: D 913 MET cc_start: 0.2987 (tmm) cc_final: 0.1907 (ttp) REVERT: H 75 MET cc_start: 0.2744 (mmp) cc_final: 0.2113 (mmt) outliers start: 98 outliers final: 80 residues processed: 450 average time/residue: 0.4751 time to fit residues: 358.0773 Evaluate side-chains 453 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 366 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 265 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 93 optimal weight: 0.0980 chunk 335 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.221517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3996 r_free = 0.3996 target = 0.161625 restraints weight = 51076.245| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.48 r_work: 0.3639 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36397 Z= 0.182 Angle : 0.561 16.109 49033 Z= 0.286 Chirality : 0.040 0.223 5235 Planarity : 0.003 0.046 6216 Dihedral : 5.925 59.533 4881 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.11 % Allowed : 28.30 % Favored : 69.59 % 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: 0.15 (0.13), residues: 4155 helix: 0.87 (0.11), residues: 2415 sheet: -0.37 (0.34), residues: 222 loop : -1.00 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 601 HIS 0.009 0.001 HIS A 978 PHE 0.023 0.001 PHE D 385 TYR 0.028 0.001 TYR B 755 ARG 0.005 0.000 ARG B 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9513.91 seconds wall clock time: 174 minutes 40.34 seconds (10480.34 seconds total)