Starting phenix.real_space_refine on Fri Feb 23 04:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8b_31013/02_2024/7e8b_31013.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 166 5.16 5 C 23614 2.51 5 N 6230 2.21 5 O 6822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 469": "OD1" <-> "OD2" Residue "K PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 469": "OD1" <-> "OD2" Residue "I TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36832 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "K" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "J" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "I" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "C" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Time building chain proxies: 19.48, per 1000 atoms: 0.53 Number of scatterers: 36832 At special positions: 0 Unit cell: (171, 161, 208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 166 16.00 O 6822 8.00 N 6230 7.00 C 23614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.04 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 784 " distance=2.03 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.04 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.19 Conformation dependent library (CDL) restraints added in 6.9 seconds 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8648 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 56 sheets defined 37.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 70 through 75 removed outlier: 3.945A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE L 75 " --> pdb=" O VAL L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 70 through 75' Processing helix chain 'L' and resid 76 through 80 removed outlier: 3.604A pdb=" N PHE L 79 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 122 removed outlier: 4.240A pdb=" N LYS L 121 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE L 122 " --> pdb=" O GLY L 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 118 through 122' Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 527 removed outlier: 4.012A pdb=" N ASN L 525 " --> pdb=" O LYS L 521 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG L 527 " --> pdb=" O ALA L 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 591 Processing helix chain 'L' and resid 608 through 613 removed outlier: 3.635A pdb=" N GLU L 613 " --> pdb=" O LYS L 609 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 632 Processing helix chain 'L' and resid 651 through 659 removed outlier: 3.629A pdb=" N LEU L 655 " --> pdb=" O TYR L 651 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.157A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 735 through 749 Processing helix chain 'L' and resid 766 through 786 removed outlier: 3.503A pdb=" N LYS L 770 " --> pdb=" O SER L 766 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS L 784 " --> pdb=" O PHE L 780 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 56 Processing helix chain 'K' and resid 71 through 80 removed outlier: 3.785A pdb=" N LEU K 74 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU K 77 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP K 78 " --> pdb=" O PHE K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 527 Processing helix chain 'K' and resid 582 through 592 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 619 through 635 removed outlier: 3.518A pdb=" N LYS K 635 " --> pdb=" O ARG K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 651 through 659 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.847A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR K 694 " --> pdb=" O PHE K 690 " (cutoff:3.500A) Processing helix chain 'K' and resid 709 through 713 removed outlier: 3.578A pdb=" N HIS K 712 " --> pdb=" O LYS K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 734 through 749 removed outlier: 4.152A pdb=" N THR K 738 " --> pdb=" O HIS K 734 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.554A pdb=" N GLU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 151 through 156 removed outlier: 4.032A pdb=" N ASP B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 228 through 251 removed outlier: 3.638A pdb=" N ALA B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.235A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.640A pdb=" N LYS B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.735A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 434 removed outlier: 4.188A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.710A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 3.736A pdb=" N TYR A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 4.054A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.414A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.676A pdb=" N CYS A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 299 removed outlier: 4.428A pdb=" N THR A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 345 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.836A pdb=" N THR A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 436 Processing helix chain 'J' and resid 32 through 56 Processing helix chain 'J' and resid 70 through 75 removed outlier: 3.945A pdb=" N LEU J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 70 through 75' Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.604A pdb=" N PHE J 79 " --> pdb=" O SER J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 122 removed outlier: 4.241A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 122 " --> pdb=" O GLY J 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 118 through 122' Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 527 removed outlier: 4.012A pdb=" N ASN J 525 " --> pdb=" O LYS J 521 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG J 527 " --> pdb=" O ALA J 523 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 591 Processing helix chain 'J' and resid 608 through 613 removed outlier: 3.634A pdb=" N GLU J 613 " --> pdb=" O LYS J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 632 Processing helix chain 'J' and resid 651 through 659 removed outlier: 3.628A pdb=" N LEU J 655 " --> pdb=" O TYR J 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.156A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 735 through 749 Processing helix chain 'J' and resid 766 through 786 removed outlier: 3.503A pdb=" N LYS J 770 " --> pdb=" O SER J 766 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 Processing helix chain 'I' and resid 71 through 80 removed outlier: 3.787A pdb=" N LEU I 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU I 77 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP I 78 " --> pdb=" O PHE I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 592 Processing helix chain 'I' and resid 607 through 612 Processing helix chain 'I' and resid 619 through 635 removed outlier: 3.519A pdb=" N LYS I 635 " --> pdb=" O ARG I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 659 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.845A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR I 694 " --> pdb=" O PHE I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 713 removed outlier: 3.577A pdb=" N HIS I 712 " --> pdb=" O LYS I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.152A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 114 through 122 removed outlier: 3.562A pdb=" N GLU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 151 through 156 removed outlier: 4.032A pdb=" N ASP D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 228 through 251 removed outlier: 3.638A pdb=" N ALA D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 removed outlier: 4.236A pdb=" N THR D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.644A pdb=" N LYS D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.735A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 434 removed outlier: 4.186A pdb=" N ASP D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 434 " --> pdb=" O LEU D 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.711A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.736A pdb=" N TYR C 115 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.054A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 131 through 150 removed outlier: 4.414A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 227 through 250 removed outlier: 3.674A pdb=" N CYS C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 299 removed outlier: 4.428A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 320 through 345 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.840A pdb=" N THR C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 436 Processing sheet with id=AA1, first strand: chain 'L' and resid 88 through 90 removed outlier: 3.551A pdb=" N SER L 90 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU L 93 " --> pdb=" O SER L 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.964A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'L' and resid 192 through 196 removed outlier: 3.679A pdb=" N TYR L 202 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE L 211 " --> pdb=" O TYR L 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'L' and resid 263 through 266 Processing sheet with id=AA7, first strand: chain 'L' and resid 319 through 326 removed outlier: 5.611A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 384 through 389 Processing sheet with id=AA9, first strand: chain 'L' and resid 425 through 432 removed outlier: 5.189A pdb=" N ILE L 428 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU L 441 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS L 437 " --> pdb=" O ASP L 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 478 through 480 removed outlier: 6.421A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.612A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL L 596 " --> pdb=" O PRO L 561 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU L 563 " --> pdb=" O VAL L 596 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS L 598 " --> pdb=" O LEU L 563 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL L 565 " --> pdb=" O CYS L 598 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR L 560 " --> pdb=" O ARG L 643 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA L 645 " --> pdb=" O TYR L 560 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU L 562 " --> pdb=" O ALA L 645 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE L 647 " --> pdb=" O LEU L 562 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU L 564 " --> pdb=" O PHE L 647 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS L 673 " --> pdb=" O THR L 642 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL L 644 " --> pdb=" O CYS L 673 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N SER L 675 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL L 646 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU L 677 " --> pdb=" O VAL L 646 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY L 674 " --> pdb=" O LEU L 723 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE L 725 " --> pdb=" O GLY L 674 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA L 676 " --> pdb=" O ILE L 725 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AB4, first strand: chain 'K' and resid 88 through 90 removed outlier: 3.552A pdb=" N GLU K 93 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 103 through 107 removed outlier: 6.851A pdb=" N VAL K 103 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 112 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AB7, first strand: chain 'K' and resid 192 through 195 removed outlier: 7.240A pdb=" N ILE K 200 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL K 213 " --> pdb=" O ILE K 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AB9, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AC1, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AC2, first strand: chain 'K' and resid 319 through 325 removed outlier: 5.646A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU K 348 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASP K 350 " --> pdb=" O CYS K 356 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS K 356 " --> pdb=" O ASP K 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 384 through 389 Processing sheet with id=AC4, first strand: chain 'K' and resid 425 through 431 removed outlier: 7.192A pdb=" N VAL K 425 " --> pdb=" O THR K 443 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR K 443 " --> pdb=" O VAL K 425 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR K 439 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU K 444 " --> pdb=" O ARG K 449 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ARG K 449 " --> pdb=" O GLU K 444 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.804A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.584A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N TYR K 560 " --> pdb=" O ARG K 641 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG K 643 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS K 673 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL K 646 " --> pdb=" O CYS K 673 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 537 through 539 Processing sheet with id=AC8, first strand: chain 'K' and resid 676 through 677 removed outlier: 6.445A pdb=" N ALA K 676 " --> pdb=" O ILE K 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.624A pdb=" N TYR B 83 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'J' and resid 88 through 90 removed outlier: 3.551A pdb=" N SER J 90 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU J 93 " --> pdb=" O SER J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.964A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AD5, first strand: chain 'J' and resid 192 through 196 removed outlier: 3.678A pdb=" N TYR J 202 " --> pdb=" O ILE J 211 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE J 211 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 242 through 244 Processing sheet with id=AD7, first strand: chain 'J' and resid 263 through 266 Processing sheet with id=AD8, first strand: chain 'J' and resid 319 through 326 removed outlier: 5.612A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 384 through 389 Processing sheet with id=AE1, first strand: chain 'J' and resid 425 through 432 removed outlier: 5.189A pdb=" N ILE J 428 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU J 441 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS J 437 " --> pdb=" O ASP J 432 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 478 through 480 removed outlier: 6.422A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.615A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL J 596 " --> pdb=" O PRO J 561 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU J 563 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N CYS J 598 " --> pdb=" O LEU J 563 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL J 565 " --> pdb=" O CYS J 598 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR J 560 " --> pdb=" O ARG J 643 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA J 645 " --> pdb=" O TYR J 560 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU J 562 " --> pdb=" O ALA J 645 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE J 647 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU J 564 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS J 673 " --> pdb=" O THR J 642 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL J 644 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N SER J 675 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL J 646 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU J 677 " --> pdb=" O VAL J 646 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY J 674 " --> pdb=" O LEU J 723 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE J 725 " --> pdb=" O GLY J 674 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA J 676 " --> pdb=" O ILE J 725 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AE5, first strand: chain 'I' and resid 88 through 90 removed outlier: 3.557A pdb=" N GLU I 93 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.852A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR I 112 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE8, first strand: chain 'I' and resid 192 through 195 removed outlier: 7.239A pdb=" N ILE I 200 " --> pdb=" O VAL I 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL I 213 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AF1, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AF2, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AF3, first strand: chain 'I' and resid 319 through 325 removed outlier: 5.649A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU I 348 " --> pdb=" O LYS I 358 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS I 358 " --> pdb=" O LEU I 348 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP I 350 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS I 356 " --> pdb=" O ASP I 350 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 384 through 389 Processing sheet with id=AF5, first strand: chain 'I' and resid 425 through 431 removed outlier: 7.300A pdb=" N VAL I 425 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR I 443 " --> pdb=" O VAL I 425 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU I 444 " --> pdb=" O ARG I 449 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ARG I 449 " --> pdb=" O GLU I 444 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.804A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.591A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR I 560 " --> pdb=" O ARG I 643 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ALA I 645 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU I 562 " --> pdb=" O ALA I 645 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE I 647 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU I 564 " --> pdb=" O PHE I 647 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS I 673 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 646 " --> pdb=" O CYS I 673 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AF9, first strand: chain 'I' and resid 676 through 677 removed outlier: 6.448A pdb=" N ALA I 676 " --> pdb=" O ILE I 725 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.613A pdb=" N TYR D 83 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 45 through 46 1531 hydrogen bonds defined for protein. 4275 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: 14.38 Time building geometry restraints manager: 17.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11830 1.34 - 1.46: 9096 1.46 - 1.58: 16562 1.58 - 1.70: 0 1.70 - 1.82: 256 Bond restraints: 37744 Sorted by residual: bond pdb=" CB PRO C 126 " pdb=" CG PRO C 126 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.72e+00 bond pdb=" CB PRO A 126 " pdb=" CG PRO A 126 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.65e+00 bond pdb=" CG PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 1.503 1.448 0.055 3.40e-02 8.65e+02 2.62e+00 bond pdb=" CG PRO C 126 " pdb=" CD PRO C 126 " ideal model delta sigma weight residual 1.503 1.449 0.054 3.40e-02 8.65e+02 2.54e+00 bond pdb=" C ILE K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 ... (remaining 37739 not shown) Histogram of bond angle deviations from ideal: 96.45 - 104.12: 516 104.12 - 111.80: 17561 111.80 - 119.47: 13701 119.47 - 127.15: 18988 127.15 - 134.83: 424 Bond angle restraints: 51190 Sorted by residual: angle pdb=" CA PRO A 126 " pdb=" N PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" CA PRO C 126 " pdb=" N PRO C 126 " pdb=" CD PRO C 126 " ideal model delta sigma weight residual 112.00 105.49 6.51 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N PRO C 126 " pdb=" CD PRO C 126 " pdb=" CG PRO C 126 " ideal model delta sigma weight residual 103.20 96.45 6.75 1.50e+00 4.44e-01 2.03e+01 angle pdb=" N PRO A 126 " pdb=" CD PRO A 126 " pdb=" CG PRO A 126 " ideal model delta sigma weight residual 103.20 96.48 6.72 1.50e+00 4.44e-01 2.01e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 115.79 110.95 4.84 1.19e+00 7.06e-01 1.65e+01 ... (remaining 51185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 20201 17.77 - 35.54: 1835 35.54 - 53.31: 370 53.31 - 71.08: 43 71.08 - 88.85: 41 Dihedral angle restraints: 22490 sinusoidal: 9042 harmonic: 13448 Sorted by residual: dihedral pdb=" CB CYS J 465 " pdb=" SG CYS J 465 " pdb=" SG CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sinusoidal sigma weight residual 93.00 16.39 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS L 465 " pdb=" SG CYS L 465 " pdb=" SG CYS L 468 " pdb=" CB CYS L 468 " ideal model delta sinusoidal sigma weight residual 93.00 16.40 76.60 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS J 474 " pdb=" SG CYS J 474 " pdb=" SG CYS J 492 " pdb=" CB CYS J 492 " ideal model delta sinusoidal sigma weight residual -86.00 -22.03 -63.97 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 22487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3988 0.040 - 0.081: 1193 0.081 - 0.121: 414 0.121 - 0.162: 49 0.162 - 0.202: 8 Chirality restraints: 5652 Sorted by residual: chirality pdb=" CB ILE J 659 " pdb=" CA ILE J 659 " pdb=" CG1 ILE J 659 " pdb=" CG2 ILE J 659 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE L 659 " pdb=" CA ILE L 659 " pdb=" CG1 ILE L 659 " pdb=" CG2 ILE L 659 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA LEU A 400 " pdb=" N LEU A 400 " pdb=" C LEU A 400 " pdb=" CB LEU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 ... (remaining 5649 not shown) Planarity restraints: 6526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 400 " -0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO C 401 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 401 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 401 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 400 " 0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 401 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 235 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ALA D 235 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA D 235 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS D 236 " -0.011 2.00e-02 2.50e+03 ... (remaining 6523 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 913 2.68 - 3.23: 37815 3.23 - 3.79: 59790 3.79 - 4.34: 79335 4.34 - 4.90: 126316 Nonbonded interactions: 304169 Sorted by model distance: nonbonded pdb=" OE2 GLU C 346 " pdb=" OG1 THR C 380 " model vdw 2.120 2.440 nonbonded pdb=" OE2 GLU A 346 " pdb=" OG1 THR A 380 " model vdw 2.120 2.440 nonbonded pdb=" OD1 ASP D 116 " pdb=" OH TYR D 137 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP B 116 " pdb=" OH TYR B 137 " model vdw 2.157 2.440 nonbonded pdb=" OH TYR I 96 " pdb=" OE1 GLN I 99 " model vdw 2.188 2.440 ... (remaining 304164 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 40 through 158 or resid 167 through 436)) selection = (chain 'B' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'C' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'D' and (resid 40 through 158 or resid 167 through 436)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.030 Extract box with map and model: 9.670 Check model and map are aligned: 0.540 Set scattering table: 0.350 Process input model: 100.410 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 37744 Z= 0.168 Angle : 0.606 9.825 51190 Z= 0.323 Chirality : 0.044 0.202 5652 Planarity : 0.004 0.099 6526 Dihedral : 14.233 88.849 13794 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.26 % Favored : 92.70 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.09 (0.12), residues: 4548 helix: 0.44 (0.14), residues: 1566 sheet: -0.48 (0.18), residues: 778 loop : -1.68 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 583 HIS 0.016 0.001 HIS D 414 PHE 0.018 0.001 PHE J 385 TYR 0.031 0.001 TYR B 363 ARG 0.005 0.000 ARG I 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 572 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 323 MET cc_start: 0.5094 (tmm) cc_final: 0.4722 (tmm) REVERT: L 424 ASP cc_start: 0.4710 (m-30) cc_final: 0.4433 (m-30) REVERT: L 475 THR cc_start: 0.6310 (p) cc_final: 0.5566 (p) REVERT: L 546 MET cc_start: 0.3925 (tmm) cc_final: 0.3500 (tmm) REVERT: L 609 LYS cc_start: 0.5489 (tptp) cc_final: 0.5016 (tppp) REVERT: L 641 ARG cc_start: 0.6026 (mpt-90) cc_final: 0.4094 (mtm180) REVERT: L 658 TYR cc_start: 0.6181 (t80) cc_final: 0.5734 (t80) REVERT: K 488 PHE cc_start: 0.6638 (p90) cc_final: 0.6410 (p90) REVERT: K 650 ASP cc_start: 0.8293 (m-30) cc_final: 0.7986 (m-30) REVERT: B 64 ASP cc_start: 0.5618 (p0) cc_final: 0.5310 (m-30) REVERT: B 98 PHE cc_start: 0.6129 (t80) cc_final: 0.5674 (t80) REVERT: B 279 MET cc_start: 0.7648 (tmm) cc_final: 0.7273 (tpp) REVERT: A 115 TYR cc_start: 0.5775 (t80) cc_final: 0.5503 (t80) REVERT: A 137 TYR cc_start: 0.6147 (t80) cc_final: 0.5730 (t80) REVERT: A 306 HIS cc_start: 0.6754 (m90) cc_final: 0.5872 (t70) REVERT: J 323 MET cc_start: 0.5085 (tmm) cc_final: 0.4713 (tmm) REVERT: J 424 ASP cc_start: 0.4726 (m-30) cc_final: 0.4450 (m-30) REVERT: J 475 THR cc_start: 0.6385 (p) cc_final: 0.5674 (p) REVERT: J 546 MET cc_start: 0.4068 (tmm) cc_final: 0.3796 (tmm) REVERT: J 609 LYS cc_start: 0.5485 (tptp) cc_final: 0.5010 (tppp) REVERT: J 641 ARG cc_start: 0.6024 (mpt-90) cc_final: 0.4095 (mtm180) REVERT: J 657 THR cc_start: 0.8140 (p) cc_final: 0.7932 (p) REVERT: J 658 TYR cc_start: 0.6166 (t80) cc_final: 0.5718 (t80) REVERT: I 488 PHE cc_start: 0.6604 (p90) cc_final: 0.6354 (p90) REVERT: I 650 ASP cc_start: 0.8284 (m-30) cc_final: 0.7976 (m-30) REVERT: D 64 ASP cc_start: 0.5663 (p0) cc_final: 0.5366 (m-30) REVERT: D 98 PHE cc_start: 0.6104 (t80) cc_final: 0.5662 (t80) REVERT: D 279 MET cc_start: 0.7626 (tmm) cc_final: 0.7256 (tpp) REVERT: C 115 TYR cc_start: 0.5760 (t80) cc_final: 0.5486 (t80) REVERT: C 137 TYR cc_start: 0.6124 (t80) cc_final: 0.5701 (t80) REVERT: C 306 HIS cc_start: 0.6781 (m90) cc_final: 0.5883 (t70) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.4834 time to fit residues: 450.0212 Evaluate side-chains 325 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 0.0010 chunk 342 optimal weight: 10.0000 chunk 190 optimal weight: 0.0000 chunk 117 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 354 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 410 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN L 606 GLN ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS K 762 HIS B 144 ASN B 408 ASN B 414 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN J 606 GLN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS I 762 HIS D 144 ASN D 408 ASN D 414 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37744 Z= 0.157 Angle : 0.563 10.727 51190 Z= 0.296 Chirality : 0.043 0.171 5652 Planarity : 0.004 0.048 6526 Dihedral : 4.324 21.220 5064 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.97 % Favored : 92.99 % Rotamer: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.86 (0.13), residues: 4548 helix: 0.78 (0.13), residues: 1602 sheet: -0.59 (0.18), residues: 812 loop : -1.64 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 244 HIS 0.006 0.001 HIS D 306 PHE 0.026 0.001 PHE C 175 TYR 0.014 0.001 TYR D 188 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 468 time to evaluate : 4.155 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: L 546 MET cc_start: 0.4158 (tmm) cc_final: 0.3913 (tmm) REVERT: L 609 LYS cc_start: 0.5514 (tptp) cc_final: 0.5186 (tppp) REVERT: L 641 ARG cc_start: 0.6128 (mpt-90) cc_final: 0.4088 (mtm180) REVERT: K 698 HIS cc_start: 0.5524 (OUTLIER) cc_final: 0.5127 (t70) REVERT: B 64 ASP cc_start: 0.5559 (p0) cc_final: 0.5298 (m-30) REVERT: B 98 PHE cc_start: 0.6000 (t80) cc_final: 0.5795 (t80) REVERT: B 247 ARG cc_start: 0.6805 (mmt90) cc_final: 0.6517 (mmm-85) REVERT: B 279 MET cc_start: 0.7416 (tmm) cc_final: 0.7137 (tpp) REVERT: B 368 MET cc_start: 0.7907 (mtp) cc_final: 0.7643 (mtp) REVERT: A 306 HIS cc_start: 0.6705 (m90) cc_final: 0.5812 (t70) REVERT: J 546 MET cc_start: 0.4186 (tmm) cc_final: 0.3900 (tmm) REVERT: J 609 LYS cc_start: 0.5512 (tptp) cc_final: 0.5180 (tppp) REVERT: J 641 ARG cc_start: 0.6133 (mpt-90) cc_final: 0.4117 (mtm180) REVERT: I 698 HIS cc_start: 0.5531 (OUTLIER) cc_final: 0.5126 (t70) REVERT: D 64 ASP cc_start: 0.5591 (p0) cc_final: 0.5345 (m-30) REVERT: D 247 ARG cc_start: 0.6795 (mmt90) cc_final: 0.6512 (mmm-85) REVERT: D 279 MET cc_start: 0.7392 (tmm) cc_final: 0.7118 (tpp) REVERT: C 306 HIS cc_start: 0.6721 (m90) cc_final: 0.5819 (t70) outliers start: 6 outliers final: 2 residues processed: 470 average time/residue: 0.4927 time to fit residues: 386.4751 Evaluate side-chains 322 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 318 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 411 optimal weight: 4.9990 chunk 444 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 407 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 329 optimal weight: 0.6980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN L 667 GLN ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN J 667 GLN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 547 GLN ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37744 Z= 0.282 Angle : 0.631 7.900 51190 Z= 0.334 Chirality : 0.045 0.159 5652 Planarity : 0.005 0.053 6526 Dihedral : 4.657 21.628 5064 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.08 (0.12), residues: 4548 helix: 0.64 (0.13), residues: 1584 sheet: -0.83 (0.18), residues: 824 loop : -1.73 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 229 HIS 0.015 0.001 HIS B 414 PHE 0.030 0.002 PHE I 481 TYR 0.017 0.002 TYR I 282 ARG 0.007 0.001 ARG J 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 609 LYS cc_start: 0.5521 (tptp) cc_final: 0.5243 (tppp) REVERT: L 641 ARG cc_start: 0.6054 (mpt-90) cc_final: 0.4147 (mtm180) REVERT: K 341 GLN cc_start: 0.5582 (pt0) cc_final: 0.5219 (pt0) REVERT: B 62 TYR cc_start: 0.4072 (m-80) cc_final: 0.3860 (m-80) REVERT: B 64 ASP cc_start: 0.5560 (p0) cc_final: 0.5303 (m-30) REVERT: B 148 LEU cc_start: 0.8679 (mp) cc_final: 0.8051 (tt) REVERT: B 247 ARG cc_start: 0.6957 (mmt90) cc_final: 0.6613 (mmm-85) REVERT: B 368 MET cc_start: 0.8042 (mtp) cc_final: 0.7828 (mtp) REVERT: A 306 HIS cc_start: 0.6784 (m90) cc_final: 0.5793 (t70) REVERT: J 546 MET cc_start: 0.4350 (tmm) cc_final: 0.4069 (tmm) REVERT: J 609 LYS cc_start: 0.5520 (tptp) cc_final: 0.5243 (tppp) REVERT: J 641 ARG cc_start: 0.6039 (mpt-90) cc_final: 0.4126 (mtm180) REVERT: I 633 MET cc_start: 0.6539 (mmt) cc_final: 0.6174 (mmt) REVERT: D 62 TYR cc_start: 0.4068 (m-80) cc_final: 0.3859 (m-80) REVERT: D 64 ASP cc_start: 0.5569 (p0) cc_final: 0.5318 (m-30) REVERT: D 148 LEU cc_start: 0.8689 (mp) cc_final: 0.8057 (tt) REVERT: D 247 ARG cc_start: 0.6962 (mmt90) cc_final: 0.6622 (mmm-85) REVERT: C 306 HIS cc_start: 0.6813 (m90) cc_final: 0.5804 (t70) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.4788 time to fit residues: 328.6679 Evaluate side-chains 296 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 412 optimal weight: 0.8980 chunk 436 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 391 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 304 HIS ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS ** I 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37744 Z= 0.271 Angle : 0.628 8.571 51190 Z= 0.332 Chirality : 0.045 0.168 5652 Planarity : 0.005 0.052 6526 Dihedral : 4.804 23.015 5064 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.40 % Favored : 91.56 % Rotamer: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.20 (0.12), residues: 4548 helix: 0.68 (0.13), residues: 1548 sheet: -0.82 (0.18), residues: 798 loop : -1.90 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 229 HIS 0.008 0.001 HIS I 304 PHE 0.041 0.002 PHE D 295 TYR 0.018 0.002 TYR D 188 ARG 0.009 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 4.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.5810 (mm) cc_final: 0.5482 (pt) REVERT: L 485 MET cc_start: 0.4786 (mpp) cc_final: 0.4580 (mpp) REVERT: L 609 LYS cc_start: 0.5686 (tptp) cc_final: 0.5273 (tppp) REVERT: L 641 ARG cc_start: 0.5968 (mpt-90) cc_final: 0.4122 (mtm180) REVERT: K 341 GLN cc_start: 0.5878 (pt0) cc_final: 0.5677 (pt0) REVERT: K 698 HIS cc_start: 0.5477 (OUTLIER) cc_final: 0.4883 (t70) REVERT: B 64 ASP cc_start: 0.5464 (p0) cc_final: 0.5228 (m-30) REVERT: B 247 ARG cc_start: 0.6969 (mmt90) cc_final: 0.6617 (mmm-85) REVERT: B 368 MET cc_start: 0.8077 (mtp) cc_final: 0.7846 (mtp) REVERT: A 202 ASN cc_start: 0.6920 (m-40) cc_final: 0.6352 (t0) REVERT: A 306 HIS cc_start: 0.6885 (m90) cc_final: 0.5848 (t70) REVERT: J 240 ILE cc_start: 0.5787 (mm) cc_final: 0.5465 (pt) REVERT: J 485 MET cc_start: 0.4809 (mpp) cc_final: 0.4605 (mpp) REVERT: J 564 LEU cc_start: 0.6746 (tt) cc_final: 0.6178 (mt) REVERT: J 609 LYS cc_start: 0.5679 (tptp) cc_final: 0.5259 (tppp) REVERT: J 641 ARG cc_start: 0.5906 (mpt-90) cc_final: 0.4104 (mtm180) REVERT: I 633 MET cc_start: 0.6609 (mmt) cc_final: 0.6249 (mmt) REVERT: I 698 HIS cc_start: 0.5467 (OUTLIER) cc_final: 0.4868 (t70) REVERT: D 64 ASP cc_start: 0.5445 (p0) cc_final: 0.5231 (m-30) REVERT: D 247 ARG cc_start: 0.6987 (mmt90) cc_final: 0.6624 (mmm-85) REVERT: C 202 ASN cc_start: 0.6907 (m-40) cc_final: 0.6347 (t0) REVERT: C 306 HIS cc_start: 0.6923 (m90) cc_final: 0.5862 (t70) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.4975 time to fit residues: 343.6369 Evaluate side-chains 298 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 296 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 372 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 223 optimal weight: 0.2980 chunk 392 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 304 HIS ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 734 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 734 HIS ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37744 Z= 0.231 Angle : 0.606 7.176 51190 Z= 0.320 Chirality : 0.044 0.162 5652 Planarity : 0.004 0.052 6526 Dihedral : 4.737 21.886 5064 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.14 (0.12), residues: 4548 helix: 0.69 (0.13), residues: 1554 sheet: -0.77 (0.19), residues: 794 loop : -1.86 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 336 HIS 0.006 0.001 HIS J 612 PHE 0.030 0.002 PHE D 187 TYR 0.016 0.002 TYR B 188 ARG 0.006 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 4.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.5935 (mm) cc_final: 0.5641 (pt) REVERT: L 564 LEU cc_start: 0.6613 (tt) cc_final: 0.6006 (mt) REVERT: L 609 LYS cc_start: 0.5649 (tptp) cc_final: 0.5282 (tptm) REVERT: L 641 ARG cc_start: 0.6118 (mpt-90) cc_final: 0.4323 (mtm180) REVERT: K 264 MET cc_start: 0.7544 (tpp) cc_final: 0.6737 (tpp) REVERT: K 633 MET cc_start: 0.6603 (mmt) cc_final: 0.6289 (mmt) REVERT: B 64 ASP cc_start: 0.5469 (p0) cc_final: 0.5159 (m-30) REVERT: B 148 LEU cc_start: 0.8618 (mp) cc_final: 0.7950 (tt) REVERT: B 247 ARG cc_start: 0.6930 (mmt90) cc_final: 0.6489 (mmm-85) REVERT: A 202 ASN cc_start: 0.6825 (m-40) cc_final: 0.6382 (t0) REVERT: A 306 HIS cc_start: 0.6864 (m90) cc_final: 0.5832 (t70) REVERT: A 389 ILE cc_start: 0.9364 (mt) cc_final: 0.8980 (mm) REVERT: J 240 ILE cc_start: 0.5910 (mm) cc_final: 0.5627 (pt) REVERT: J 546 MET cc_start: 0.4169 (tmm) cc_final: 0.3875 (tmm) REVERT: J 564 LEU cc_start: 0.6794 (tt) cc_final: 0.6157 (mt) REVERT: J 609 LYS cc_start: 0.5650 (tptp) cc_final: 0.5277 (tptm) REVERT: J 641 ARG cc_start: 0.6097 (mpt-90) cc_final: 0.4319 (mtm180) REVERT: I 264 MET cc_start: 0.7543 (tpp) cc_final: 0.6742 (tpp) REVERT: I 633 MET cc_start: 0.6528 (mmt) cc_final: 0.6200 (mmt) REVERT: D 64 ASP cc_start: 0.5449 (p0) cc_final: 0.5202 (m-30) REVERT: D 148 LEU cc_start: 0.8634 (mp) cc_final: 0.7959 (tt) REVERT: D 247 ARG cc_start: 0.6930 (mmt90) cc_final: 0.6470 (mmm-85) REVERT: C 202 ASN cc_start: 0.6807 (m-40) cc_final: 0.6373 (t0) REVERT: C 306 HIS cc_start: 0.6877 (m90) cc_final: 0.5850 (t70) REVERT: C 389 ILE cc_start: 0.9249 (mt) cc_final: 0.8880 (mm) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.4670 time to fit residues: 313.8825 Evaluate side-chains 293 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 0.8980 chunk 393 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 437 optimal weight: 20.0000 chunk 363 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37744 Z= 0.159 Angle : 0.577 7.387 51190 Z= 0.301 Chirality : 0.044 0.189 5652 Planarity : 0.004 0.051 6526 Dihedral : 4.519 20.970 5064 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.12 % Favored : 92.79 % Rotamer: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.99 (0.12), residues: 4548 helix: 0.73 (0.13), residues: 1580 sheet: -0.70 (0.18), residues: 810 loop : -1.71 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 336 HIS 0.010 0.001 HIS I 304 PHE 0.031 0.002 PHE L 785 TYR 0.027 0.001 TYR D 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 5.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.5972 (mm) cc_final: 0.5654 (pt) REVERT: L 309 MET cc_start: 0.7052 (tpp) cc_final: 0.6664 (tpp) REVERT: L 564 LEU cc_start: 0.6560 (tt) cc_final: 0.5997 (mt) REVERT: L 609 LYS cc_start: 0.5578 (tptp) cc_final: 0.5204 (tptm) REVERT: L 641 ARG cc_start: 0.6218 (mpt-90) cc_final: 0.4333 (mtm180) REVERT: L 658 TYR cc_start: 0.6514 (t80) cc_final: 0.5829 (t80) REVERT: K 264 MET cc_start: 0.7361 (tpp) cc_final: 0.6668 (tpp) REVERT: K 633 MET cc_start: 0.6533 (mmt) cc_final: 0.6243 (mmt) REVERT: K 698 HIS cc_start: 0.5352 (OUTLIER) cc_final: 0.4846 (t70) REVERT: B 64 ASP cc_start: 0.5361 (p0) cc_final: 0.5036 (m-30) REVERT: B 173 ARG cc_start: 0.6494 (tmm-80) cc_final: 0.5965 (ttp-170) REVERT: B 247 ARG cc_start: 0.6667 (mmt90) cc_final: 0.6362 (mmm-85) REVERT: A 306 HIS cc_start: 0.6810 (m90) cc_final: 0.5735 (t70) REVERT: A 389 ILE cc_start: 0.9216 (mt) cc_final: 0.8926 (mm) REVERT: J 240 ILE cc_start: 0.5945 (mm) cc_final: 0.5634 (pt) REVERT: J 309 MET cc_start: 0.7036 (tpp) cc_final: 0.6653 (tpp) REVERT: J 546 MET cc_start: 0.4088 (tmm) cc_final: 0.3770 (tmm) REVERT: J 564 LEU cc_start: 0.6626 (tt) cc_final: 0.5970 (mt) REVERT: J 609 LYS cc_start: 0.5545 (tptp) cc_final: 0.5181 (tptm) REVERT: J 641 ARG cc_start: 0.6197 (mpt-90) cc_final: 0.4337 (mtm180) REVERT: J 658 TYR cc_start: 0.6526 (t80) cc_final: 0.5879 (t80) REVERT: I 264 MET cc_start: 0.7356 (tpp) cc_final: 0.6670 (tpp) REVERT: I 633 MET cc_start: 0.6518 (mmt) cc_final: 0.6222 (mmt) REVERT: D 64 ASP cc_start: 0.5440 (p0) cc_final: 0.5078 (m-30) REVERT: D 247 ARG cc_start: 0.6665 (mmt90) cc_final: 0.6356 (mmm-85) REVERT: C 306 HIS cc_start: 0.6830 (m90) cc_final: 0.5752 (t70) REVERT: C 389 ILE cc_start: 0.9083 (mt) cc_final: 0.8812 (mm) outliers start: 2 outliers final: 1 residues processed: 432 average time/residue: 0.4748 time to fit residues: 342.6539 Evaluate side-chains 306 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 304 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 435 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 37744 Z= 0.301 Angle : 0.659 7.744 51190 Z= 0.350 Chirality : 0.046 0.189 5652 Planarity : 0.005 0.053 6526 Dihedral : 4.848 22.858 5064 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.77 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.28 (0.12), residues: 4548 helix: 0.56 (0.13), residues: 1566 sheet: -0.97 (0.18), residues: 800 loop : -1.88 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 423 HIS 0.008 0.001 HIS L 612 PHE 0.035 0.003 PHE L 785 TYR 0.023 0.002 TYR I 149 ARG 0.006 0.001 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 609 LYS cc_start: 0.5683 (tptp) cc_final: 0.5286 (tptm) REVERT: L 641 ARG cc_start: 0.6215 (mpt-90) cc_final: 0.4512 (mtp180) REVERT: K 308 MET cc_start: 0.6429 (mpp) cc_final: 0.6210 (mpp) REVERT: K 633 MET cc_start: 0.6464 (mmt) cc_final: 0.6128 (mmt) REVERT: B 64 ASP cc_start: 0.5447 (p0) cc_final: 0.5097 (m-30) REVERT: B 148 LEU cc_start: 0.8671 (mp) cc_final: 0.7896 (tt) REVERT: B 173 ARG cc_start: 0.6614 (tmm-80) cc_final: 0.6118 (ttp-170) REVERT: B 247 ARG cc_start: 0.6803 (mmt90) cc_final: 0.6268 (mmm-85) REVERT: A 306 HIS cc_start: 0.7220 (m90) cc_final: 0.5985 (t70) REVERT: J 546 MET cc_start: 0.4103 (tmm) cc_final: 0.3580 (tmm) REVERT: J 564 LEU cc_start: 0.6745 (tt) cc_final: 0.6187 (tp) REVERT: J 609 LYS cc_start: 0.5650 (tptp) cc_final: 0.5275 (tptm) REVERT: J 641 ARG cc_start: 0.6198 (mpt-90) cc_final: 0.4484 (mtp180) REVERT: I 308 MET cc_start: 0.6402 (mpp) cc_final: 0.6178 (mpp) REVERT: I 633 MET cc_start: 0.6600 (mmt) cc_final: 0.6239 (mmt) REVERT: D 64 ASP cc_start: 0.5519 (p0) cc_final: 0.5119 (m-30) REVERT: D 148 LEU cc_start: 0.8691 (mp) cc_final: 0.7911 (tt) REVERT: D 247 ARG cc_start: 0.6752 (mmt90) cc_final: 0.6229 (mmm-85) REVERT: C 306 HIS cc_start: 0.7252 (m90) cc_final: 0.6003 (t70) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.4716 time to fit residues: 303.6248 Evaluate side-chains 274 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 84 optimal weight: 0.3980 chunk 276 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37744 Z= 0.185 Angle : 0.606 13.128 51190 Z= 0.314 Chirality : 0.044 0.172 5652 Planarity : 0.004 0.050 6526 Dihedral : 4.674 22.843 5064 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.10 (0.12), residues: 4548 helix: 0.69 (0.13), residues: 1560 sheet: -0.82 (0.18), residues: 816 loop : -1.78 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 185 HIS 0.007 0.001 HIS K 304 PHE 0.028 0.002 PHE L 785 TYR 0.020 0.001 TYR K 149 ARG 0.004 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6201 (mm) cc_final: 0.5816 (pt) REVERT: L 609 LYS cc_start: 0.5657 (tptp) cc_final: 0.5274 (tptm) REVERT: L 641 ARG cc_start: 0.6329 (mpt-90) cc_final: 0.4563 (mtp180) REVERT: K 633 MET cc_start: 0.6449 (mmt) cc_final: 0.6092 (mmt) REVERT: K 698 HIS cc_start: 0.5499 (OUTLIER) cc_final: 0.5100 (t70) REVERT: B 64 ASP cc_start: 0.5393 (p0) cc_final: 0.5060 (m-30) REVERT: B 148 LEU cc_start: 0.8599 (mp) cc_final: 0.7896 (tt) REVERT: B 173 ARG cc_start: 0.6590 (tmm-80) cc_final: 0.5987 (ttp-170) REVERT: B 247 ARG cc_start: 0.6703 (mmt90) cc_final: 0.6237 (mmm-85) REVERT: A 306 HIS cc_start: 0.7144 (m90) cc_final: 0.5936 (t70) REVERT: J 240 ILE cc_start: 0.6173 (mm) cc_final: 0.5797 (pt) REVERT: J 546 MET cc_start: 0.4051 (tmm) cc_final: 0.3671 (tmm) REVERT: J 564 LEU cc_start: 0.6665 (tt) cc_final: 0.6117 (tp) REVERT: J 609 LYS cc_start: 0.5634 (tptp) cc_final: 0.5255 (tptm) REVERT: J 641 ARG cc_start: 0.6310 (mpt-90) cc_final: 0.4529 (mtp180) REVERT: J 658 TYR cc_start: 0.6617 (t80) cc_final: 0.5901 (t80) REVERT: I 633 MET cc_start: 0.6539 (mmt) cc_final: 0.6202 (mmt) REVERT: I 698 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.5024 (t70) REVERT: D 64 ASP cc_start: 0.5346 (p0) cc_final: 0.5000 (m-30) REVERT: D 148 LEU cc_start: 0.8590 (mp) cc_final: 0.7871 (tt) REVERT: D 247 ARG cc_start: 0.6652 (mmt90) cc_final: 0.6208 (mmm-85) REVERT: C 306 HIS cc_start: 0.7177 (m90) cc_final: 0.5949 (t70) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.4523 time to fit residues: 300.5973 Evaluate side-chains 288 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 5.9990 chunk 417 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 405 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 404 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN L 369 HIS ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN J 369 HIS ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37744 Z= 0.221 Angle : 0.617 12.091 51190 Z= 0.323 Chirality : 0.044 0.178 5652 Planarity : 0.004 0.051 6526 Dihedral : 4.701 22.622 5064 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.13 (0.12), residues: 4548 helix: 0.73 (0.13), residues: 1546 sheet: -0.85 (0.18), residues: 808 loop : -1.84 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 106 HIS 0.007 0.001 HIS D 306 PHE 0.033 0.002 PHE J 785 TYR 0.021 0.001 TYR K 149 ARG 0.003 0.000 ARG I 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6263 (mm) cc_final: 0.5835 (pt) REVERT: L 609 LYS cc_start: 0.5678 (tptp) cc_final: 0.5241 (tptm) REVERT: L 641 ARG cc_start: 0.6306 (mpt-90) cc_final: 0.4581 (mtp180) REVERT: K 323 MET cc_start: 0.3615 (tpp) cc_final: 0.3379 (tpp) REVERT: K 587 MET cc_start: 0.6668 (tpt) cc_final: 0.5979 (mmm) REVERT: K 633 MET cc_start: 0.6485 (mmt) cc_final: 0.6115 (mmt) REVERT: B 64 ASP cc_start: 0.5329 (p0) cc_final: 0.5024 (m-30) REVERT: B 148 LEU cc_start: 0.8586 (mp) cc_final: 0.7959 (tt) REVERT: B 173 ARG cc_start: 0.6700 (tmm-80) cc_final: 0.6077 (ttp-170) REVERT: B 342 MET cc_start: 0.8579 (mmm) cc_final: 0.8376 (tpp) REVERT: A 306 HIS cc_start: 0.7139 (m90) cc_final: 0.5903 (t70) REVERT: A 317 LEU cc_start: 0.8868 (mm) cc_final: 0.8555 (mm) REVERT: J 240 ILE cc_start: 0.6231 (mm) cc_final: 0.5820 (pt) REVERT: J 546 MET cc_start: 0.4191 (tmm) cc_final: 0.3722 (tmm) REVERT: J 564 LEU cc_start: 0.6709 (tt) cc_final: 0.6149 (tp) REVERT: J 609 LYS cc_start: 0.5661 (tptp) cc_final: 0.5230 (tptm) REVERT: I 308 MET cc_start: 0.6556 (mpp) cc_final: 0.6223 (mpp) REVERT: I 633 MET cc_start: 0.6577 (mmt) cc_final: 0.6330 (mmt) REVERT: D 64 ASP cc_start: 0.5302 (p0) cc_final: 0.4990 (m-30) REVERT: D 148 LEU cc_start: 0.8602 (mp) cc_final: 0.7965 (tt) REVERT: C 306 HIS cc_start: 0.7184 (m90) cc_final: 0.5921 (t70) REVERT: C 317 LEU cc_start: 0.8864 (mm) cc_final: 0.8547 (mm) REVERT: C 376 MET cc_start: 0.7416 (ptt) cc_final: 0.7147 (ptt) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.4568 time to fit residues: 290.7983 Evaluate side-chains 276 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 0.7980 chunk 429 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 450 optimal weight: 1.9990 chunk 414 optimal weight: 20.0000 chunk 358 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37744 Z= 0.191 Angle : 0.610 11.953 51190 Z= 0.317 Chirality : 0.044 0.167 5652 Planarity : 0.004 0.050 6526 Dihedral : 4.648 22.738 5064 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.08 (0.12), residues: 4548 helix: 0.75 (0.13), residues: 1548 sheet: -0.78 (0.19), residues: 804 loop : -1.80 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 423 HIS 0.006 0.001 HIS D 306 PHE 0.030 0.002 PHE C 194 TYR 0.021 0.001 TYR K 149 ARG 0.004 0.000 ARG K 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 375 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6265 (mm) cc_final: 0.5861 (pt) REVERT: L 564 LEU cc_start: 0.6769 (tt) cc_final: 0.6182 (tp) REVERT: L 609 LYS cc_start: 0.5860 (tptp) cc_final: 0.5409 (tptm) REVERT: K 323 MET cc_start: 0.3552 (tpp) cc_final: 0.3189 (tpt) REVERT: K 587 MET cc_start: 0.6639 (tpt) cc_final: 0.6054 (mmm) REVERT: K 633 MET cc_start: 0.6500 (mmt) cc_final: 0.6123 (mmt) REVERT: K 698 HIS cc_start: 0.5579 (OUTLIER) cc_final: 0.5189 (t70) REVERT: B 64 ASP cc_start: 0.5238 (p0) cc_final: 0.4935 (m-30) REVERT: B 148 LEU cc_start: 0.8601 (mp) cc_final: 0.7988 (tt) REVERT: B 173 ARG cc_start: 0.6690 (tmm-80) cc_final: 0.6064 (ttp-170) REVERT: B 247 ARG cc_start: 0.6763 (mmt90) cc_final: 0.6368 (mmm-85) REVERT: A 306 HIS cc_start: 0.7114 (m90) cc_final: 0.5887 (t70) REVERT: A 317 LEU cc_start: 0.8879 (mm) cc_final: 0.8600 (mm) REVERT: J 240 ILE cc_start: 0.6235 (mm) cc_final: 0.5849 (pt) REVERT: J 546 MET cc_start: 0.4209 (tmm) cc_final: 0.3690 (tmm) REVERT: J 564 LEU cc_start: 0.6683 (tt) cc_final: 0.6100 (tp) REVERT: J 609 LYS cc_start: 0.5843 (tptp) cc_final: 0.5395 (tptm) REVERT: I 633 MET cc_start: 0.6605 (mmt) cc_final: 0.6373 (mmt) REVERT: I 698 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.5148 (t70) REVERT: D 64 ASP cc_start: 0.5246 (p0) cc_final: 0.4937 (m-30) REVERT: D 148 LEU cc_start: 0.8617 (mp) cc_final: 0.8002 (tt) REVERT: D 247 ARG cc_start: 0.6718 (mmt90) cc_final: 0.6324 (mmm-85) REVERT: C 306 HIS cc_start: 0.7169 (m90) cc_final: 0.5884 (t70) REVERT: C 317 LEU cc_start: 0.8872 (mm) cc_final: 0.8591 (mm) REVERT: C 376 MET cc_start: 0.7348 (ptt) cc_final: 0.7092 (ptt) outliers start: 2 outliers final: 0 residues processed: 377 average time/residue: 0.4347 time to fit residues: 281.4610 Evaluate side-chains 288 residues out of total 4028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 0.4980 chunk 381 optimal weight: 7.9990 chunk 109 optimal weight: 0.0270 chunk 330 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 359 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 368 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 GLN ** K 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN B 416 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.111273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095947 restraints weight = 153668.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094156 restraints weight = 206457.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.093250 restraints weight = 156445.469| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37744 Z= 0.254 Angle : 0.639 11.664 51190 Z= 0.334 Chirality : 0.045 0.171 5652 Planarity : 0.004 0.053 6526 Dihedral : 4.785 22.946 5064 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.20 (0.12), residues: 4548 helix: 0.69 (0.13), residues: 1548 sheet: -0.94 (0.18), residues: 806 loop : -1.86 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 106 HIS 0.007 0.001 HIS D 306 PHE 0.022 0.002 PHE A 361 TYR 0.022 0.002 TYR K 149 ARG 0.005 0.000 ARG J 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7190.40 seconds wall clock time: 133 minutes 24.30 seconds (8004.30 seconds total)