Starting phenix.real_space_refine on Wed Mar 20 21:57:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/03_2024/6o72_0638.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Na 8 4.78 5 C 18776 2.51 5 N 4604 2.21 5 O 5028 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 775": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28592 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "B" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "D" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 140 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 3, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 14.88, per 1000 atoms: 0.52 Number of scatterers: 28592 At special positions: 0 Unit cell: (128.139, 128.139, 145.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 148 16.00 P 4 15.00 Na 8 11.00 F 24 9.00 O 5028 8.00 N 4604 7.00 C 18776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.52 Conformation dependent library (CDL) restraints added in 5.1 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 8 sheets defined 70.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 724 through 749 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP A 787 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET A 849 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 879 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'A' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1014 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1089 through 1094' Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.709A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 358' Processing helix chain 'B' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 393 through 409 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.676A pdb=" N ASN B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.519A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.797A pdb=" N LYS B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY B 697 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 724 through 749 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP B 787 " --> pdb=" O TYR B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 806 removed outlier: 3.805A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET B 849 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 879 Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.594A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 994 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 Processing helix chain 'B' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B1014 " --> pdb=" O TYR B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1087 Processing helix chain 'B' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1089 through 1094' Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.711A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 361 through 374 removed outlier: 4.092A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 393 through 409 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.579A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.889A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY C 697 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 722 Processing helix chain 'C' and resid 724 through 749 Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP C 787 " --> pdb=" O TYR C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 799 " --> pdb=" O LEU C 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET C 849 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 879 Processing helix chain 'C' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.281A pdb=" N TYR C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS C 951 " --> pdb=" O ILE C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.732A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 995 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1005 Processing helix chain 'C' and resid 1006 through 1014 removed outlier: 4.324A pdb=" N PHE C1012 " --> pdb=" O PHE C1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C1014 " --> pdb=" O TYR C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1059 removed outlier: 3.529A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG C1071 " --> pdb=" O GLU C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1087 Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1089 through 1094' Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 4.185A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 358' Processing helix chain 'D' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 393 through 409 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN D 501 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY D 697 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 722 Processing helix chain 'D' and resid 724 through 749 Processing helix chain 'D' and resid 756 through 766 Processing helix chain 'D' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP D 787 " --> pdb=" O TYR D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 799 " --> pdb=" O LEU D 795 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 806 " --> pdb=" O ALA D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 842 " --> pdb=" O THR D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET D 849 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 879 Processing helix chain 'D' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR D 898 " --> pdb=" O ILE D 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS D 951 " --> pdb=" O ILE D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 994 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 995 " --> pdb=" O LEU D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1005 Processing helix chain 'D' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE D1012 " --> pdb=" O PHE D1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG D1071 " --> pdb=" O GLU D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1087 Processing helix chain 'D' and resid 1089 through 1094 removed outlier: 3.581A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1089 through 1094' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 170 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 205 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 172 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 292 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE B 170 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 205 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 172 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 292 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE C 170 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 205 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 172 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 292 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 170 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 205 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 172 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 292 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 4320 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: 9.92 Time building geometry restraints manager: 12.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4480 1.31 - 1.44: 8218 1.44 - 1.56: 16246 1.56 - 1.69: 48 1.69 - 1.82: 244 Bond restraints: 29236 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C19 T14 C1305 " pdb=" N20 T14 C1305 " ideal model delta sigma weight residual 1.274 1.446 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 29231 not shown) Histogram of bond angle deviations from ideal: 95.27 - 104.60: 340 104.60 - 113.93: 16864 113.93 - 123.26: 21043 123.26 - 132.59: 1161 132.59 - 141.92: 108 Bond angle restraints: 39516 Sorted by residual: angle pdb=" C PHE B1003 " pdb=" N PRO B1004 " pdb=" CA PRO B1004 " ideal model delta sigma weight residual 119.87 108.20 11.67 1.04e+00 9.25e-01 1.26e+02 angle pdb=" C PHE A1003 " pdb=" N PRO A1004 " pdb=" CA PRO A1004 " ideal model delta sigma weight residual 119.87 108.22 11.65 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE C1003 " pdb=" N PRO C1004 " pdb=" CA PRO C1004 " ideal model delta sigma weight residual 119.87 108.23 11.64 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE D1003 " pdb=" N PRO D1004 " pdb=" CA PRO D1004 " ideal model delta sigma weight residual 119.87 108.25 11.62 1.04e+00 9.25e-01 1.25e+02 angle pdb=" N HIS B 412 " pdb=" CA HIS B 412 " pdb=" C HIS B 412 " ideal model delta sigma weight residual 112.92 99.93 12.99 1.23e+00 6.61e-01 1.12e+02 ... (remaining 39511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 16775 31.24 - 62.47: 637 62.47 - 93.71: 56 93.71 - 124.95: 4 124.95 - 156.19: 4 Dihedral angle restraints: 17476 sinusoidal: 7408 harmonic: 10068 Sorted by residual: dihedral pdb=" CA SER D 638 " pdb=" C SER D 638 " pdb=" N CYS D 639 " pdb=" CA CYS D 639 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER A 638 " pdb=" C SER A 638 " pdb=" N CYS A 639 " pdb=" CA CYS A 639 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N CYS C 639 " pdb=" CA CYS C 639 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4117 0.101 - 0.202: 255 0.202 - 0.304: 19 0.304 - 0.405: 5 0.405 - 0.506: 4 Chirality restraints: 4400 Sorted by residual: chirality pdb=" CBI Y01 B1301 " pdb=" CAU Y01 B1301 " pdb=" CBE Y01 B1301 " pdb=" CBG Y01 B1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4397 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 947 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 947 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 947 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 948 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.047 5.00e-02 4.00e+02 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 293 2.63 - 3.20: 24432 3.20 - 3.76: 44890 3.76 - 4.33: 64913 4.33 - 4.90: 101723 Nonbonded interactions: 236251 Sorted by model distance: nonbonded pdb=" O TYR D 286 " pdb=" O GLY D 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR C 286 " pdb=" O GLY C 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR A 286 " pdb=" O GLY A 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR B 286 " pdb=" O GLY B 288 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR B 115 " pdb=" OD1 ASP B 116 " model vdw 2.291 2.440 ... (remaining 236246 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 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'B' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'C' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'D' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.160 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 74.390 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.357 29236 Z= 0.562 Angle : 1.197 23.439 39516 Z= 0.617 Chirality : 0.059 0.506 4400 Planarity : 0.007 0.084 4816 Dihedral : 16.340 156.185 10924 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.25 (0.08), residues: 3336 helix: -4.15 (0.05), residues: 2240 sheet: -2.60 (0.35), residues: 176 loop : -3.67 (0.15), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 984 HIS 0.005 0.001 HIS C 129 PHE 0.033 0.002 PHE D 700 TYR 0.015 0.002 TYR C 286 ARG 0.013 0.001 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 837 time to evaluate : 3.468 Fit side-chains REVERT: A 161 TYR cc_start: 0.8111 (t80) cc_final: 0.7625 (t80) REVERT: A 281 ILE cc_start: 0.8487 (tt) cc_final: 0.7496 (tt) REVERT: A 422 LYS cc_start: 0.8770 (mttt) cc_final: 0.8382 (mttp) REVERT: A 426 GLU cc_start: 0.7664 (tp30) cc_final: 0.7100 (tp30) REVERT: A 440 ASN cc_start: 0.7643 (m-40) cc_final: 0.7405 (m110) REVERT: A 565 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8387 (tttp) REVERT: A 611 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 734 ILE cc_start: 0.9053 (mt) cc_final: 0.8812 (mm) REVERT: A 772 ASP cc_start: 0.8093 (t0) cc_final: 0.7520 (t0) REVERT: B 281 ILE cc_start: 0.8545 (tt) cc_final: 0.7525 (tt) REVERT: B 426 GLU cc_start: 0.7839 (tp30) cc_final: 0.7219 (tp30) REVERT: B 440 ASN cc_start: 0.7731 (m-40) cc_final: 0.7426 (m110) REVERT: B 604 GLU cc_start: 0.7933 (pt0) cc_final: 0.7699 (pt0) REVERT: B 611 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 793 ASP cc_start: 0.7906 (m-30) cc_final: 0.7697 (m-30) REVERT: B 1001 ILE cc_start: 0.8668 (mt) cc_final: 0.8384 (pp) REVERT: C 161 TYR cc_start: 0.8148 (t80) cc_final: 0.7947 (t80) REVERT: C 211 ILE cc_start: 0.8118 (pt) cc_final: 0.7914 (pp) REVERT: C 281 ILE cc_start: 0.8523 (tt) cc_final: 0.7507 (tt) REVERT: C 426 GLU cc_start: 0.7821 (tp30) cc_final: 0.7220 (tp30) REVERT: C 440 ASN cc_start: 0.7704 (m-40) cc_final: 0.7419 (m110) REVERT: C 596 LYS cc_start: 0.8461 (mttp) cc_final: 0.8246 (mttp) REVERT: C 604 GLU cc_start: 0.7931 (pt0) cc_final: 0.7698 (pt0) REVERT: C 611 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 793 ASP cc_start: 0.7906 (m-30) cc_final: 0.7700 (m-30) REVERT: D 211 ILE cc_start: 0.8119 (pt) cc_final: 0.7904 (pp) REVERT: D 281 ILE cc_start: 0.8576 (tt) cc_final: 0.7616 (tt) REVERT: D 422 LYS cc_start: 0.8708 (mttt) cc_final: 0.8283 (mttp) REVERT: D 426 GLU cc_start: 0.7853 (tp30) cc_final: 0.7236 (tp30) REVERT: D 440 ASN cc_start: 0.7790 (m-40) cc_final: 0.7495 (m110) REVERT: D 604 GLU cc_start: 0.7940 (pt0) cc_final: 0.7710 (pt0) REVERT: D 611 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 0 outliers final: 2 residues processed: 837 average time/residue: 1.2049 time to fit residues: 1197.5600 Evaluate side-chains 604 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 602 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain D residue 276 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 308 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 491 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 987 GLN A1070 HIS B 297 GLN B 418 ASN B 429 GLN B 491 ASN B 851 GLN B 987 GLN C 297 GLN C 418 ASN C 429 GLN C 491 ASN C 851 GLN C 987 GLN D 297 GLN D 429 GLN D 491 ASN D 597 ASN D 851 GLN D 987 GLN D1070 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29236 Z= 0.219 Angle : 0.673 9.243 39516 Z= 0.347 Chirality : 0.042 0.206 4400 Planarity : 0.005 0.058 4816 Dihedral : 11.354 143.240 4260 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.68 % Allowed : 18.03 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.12), residues: 3336 helix: -1.77 (0.09), residues: 2264 sheet: -2.32 (0.36), residues: 176 loop : -3.15 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 867 HIS 0.007 0.001 HIS B 176 PHE 0.017 0.001 PHE C 751 TYR 0.038 0.002 TYR B 286 ARG 0.006 0.000 ARG C 998 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 688 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7877 (t80) cc_final: 0.7567 (t80) REVERT: A 164 GLN cc_start: 0.7912 (tp40) cc_final: 0.7624 (tp40) REVERT: A 274 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7916 (tppt) REVERT: A 649 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 772 ASP cc_start: 0.8237 (t0) cc_final: 0.8034 (t0) REVERT: A 879 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6900 (pp) REVERT: B 161 TYR cc_start: 0.8107 (t80) cc_final: 0.7828 (t80) REVERT: B 190 ASN cc_start: 0.8357 (t0) cc_final: 0.8146 (OUTLIER) REVERT: B 374 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: B 386 LYS cc_start: 0.7963 (tppt) cc_final: 0.7483 (tppt) REVERT: B 498 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8345 (tttm) REVERT: B 604 GLU cc_start: 0.7955 (pt0) cc_final: 0.7676 (pt0) REVERT: B 772 ASP cc_start: 0.8199 (t0) cc_final: 0.7674 (t0) REVERT: B 776 GLN cc_start: 0.6769 (mp10) cc_final: 0.6568 (mp10) REVERT: B 879 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6760 (pp) REVERT: B 984 TRP cc_start: 0.7617 (OUTLIER) cc_final: 0.7231 (t60) REVERT: C 161 TYR cc_start: 0.8085 (t80) cc_final: 0.7782 (t80) REVERT: C 164 GLN cc_start: 0.7880 (tp40) cc_final: 0.7597 (tp40) REVERT: C 211 ILE cc_start: 0.8090 (pt) cc_final: 0.7873 (pp) REVERT: C 596 LYS cc_start: 0.8443 (mttp) cc_final: 0.8146 (mttp) REVERT: C 604 GLU cc_start: 0.7975 (pt0) cc_final: 0.7698 (pt0) REVERT: C 672 GLN cc_start: 0.8316 (mt0) cc_final: 0.8056 (tp40) REVERT: C 879 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6880 (pp) REVERT: C 953 TYR cc_start: 0.8024 (m-80) cc_final: 0.7810 (m-80) REVERT: C 984 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.7269 (t60) REVERT: C 993 GLN cc_start: 0.8201 (tt0) cc_final: 0.7943 (tt0) REVERT: D 604 GLU cc_start: 0.7989 (pt0) cc_final: 0.7712 (pt0) REVERT: D 772 ASP cc_start: 0.7972 (t0) cc_final: 0.7515 (t0) REVERT: D 953 TYR cc_start: 0.8045 (m-80) cc_final: 0.7812 (m-80) REVERT: D 984 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.7241 (t60) REVERT: D 993 GLN cc_start: 0.8209 (tt0) cc_final: 0.7877 (tp40) outliers start: 113 outliers final: 61 residues processed: 742 average time/residue: 1.1198 time to fit residues: 997.5334 Evaluate side-chains 642 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 575 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 309 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 250 HIS A 297 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 250 HIS B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B1070 HIS C 248 HIS C 250 HIS C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 776 GLN C1070 HIS D 248 HIS D 250 HIS D 297 GLN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 646 ASN D 876 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29236 Z= 0.388 Angle : 0.713 10.989 39516 Z= 0.367 Chirality : 0.046 0.177 4400 Planarity : 0.005 0.054 4816 Dihedral : 11.289 136.711 4256 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.70 % Allowed : 20.61 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.13), residues: 3336 helix: -0.81 (0.10), residues: 2268 sheet: -2.18 (0.36), residues: 176 loop : -2.89 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 888 HIS 0.007 0.001 HIS A 129 PHE 0.021 0.002 PHE B1003 TYR 0.040 0.002 TYR B 286 ARG 0.006 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 634 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8484 (ttpt) cc_final: 0.7811 (mmmt) REVERT: A 374 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 426 GLU cc_start: 0.8087 (tp30) cc_final: 0.7681 (tp30) REVERT: B 137 ILE cc_start: 0.8500 (pt) cc_final: 0.8236 (pt) REVERT: B 274 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7852 (mmmt) REVERT: B 426 GLU cc_start: 0.8087 (tp30) cc_final: 0.7701 (tp30) REVERT: B 648 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 876 GLN cc_start: 0.7705 (tt0) cc_final: 0.7457 (tt0) REVERT: C 211 ILE cc_start: 0.8247 (pt) cc_final: 0.8024 (pp) REVERT: C 274 LYS cc_start: 0.8414 (ttpt) cc_final: 0.7839 (mmmt) REVERT: C 426 GLU cc_start: 0.8099 (tp30) cc_final: 0.7707 (tp30) REVERT: C 596 LYS cc_start: 0.8631 (mttp) cc_final: 0.8364 (mttp) REVERT: C 648 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8628 (mp) REVERT: C 676 GLU cc_start: 0.7824 (tp30) cc_final: 0.7356 (mp0) REVERT: C 876 GLN cc_start: 0.7669 (tt0) cc_final: 0.7411 (tt0) REVERT: C 953 TYR cc_start: 0.8114 (m-80) cc_final: 0.7875 (m-80) REVERT: D 200 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (p) REVERT: D 274 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7771 (mmmt) REVERT: D 386 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8220 (tppt) REVERT: D 426 GLU cc_start: 0.8100 (tp30) cc_final: 0.7708 (tp30) REVERT: D 439 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7937 (m) REVERT: D 440 ASN cc_start: 0.7845 (m-40) cc_final: 0.7498 (m110) REVERT: D 648 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8617 (mp) REVERT: D 772 ASP cc_start: 0.8298 (t0) cc_final: 0.8090 (t0) REVERT: D 953 TYR cc_start: 0.8125 (m-80) cc_final: 0.7918 (m-80) outliers start: 175 outliers final: 94 residues processed: 704 average time/residue: 1.1104 time to fit residues: 944.3901 Evaluate side-chains 680 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 580 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 854 MET Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 0.0070 chunk 310 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 294 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 380 HIS B 993 GLN C 297 GLN C 597 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29236 Z= 0.198 Angle : 0.610 9.377 39516 Z= 0.314 Chirality : 0.041 0.179 4400 Planarity : 0.004 0.064 4816 Dihedral : 10.538 114.718 4256 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.59 % Allowed : 23.11 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3336 helix: -0.17 (0.11), residues: 2300 sheet: -2.12 (0.35), residues: 176 loop : -2.63 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 888 HIS 0.005 0.001 HIS C 176 PHE 0.016 0.001 PHE D 751 TYR 0.035 0.002 TYR B 286 ARG 0.009 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 689 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7734 (mmmt) REVERT: A 374 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 426 GLU cc_start: 0.8071 (tp30) cc_final: 0.7689 (tp30) REVERT: A 672 GLN cc_start: 0.8260 (mt0) cc_final: 0.7995 (tp40) REVERT: A 971 TYR cc_start: 0.8675 (p90) cc_final: 0.8440 (p90) REVERT: B 274 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7963 (tppt) REVERT: B 426 GLU cc_start: 0.8021 (tp30) cc_final: 0.7679 (tp30) REVERT: B 876 GLN cc_start: 0.7691 (tt0) cc_final: 0.7461 (tt0) REVERT: C 200 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8460 (p) REVERT: C 211 ILE cc_start: 0.8081 (pt) cc_final: 0.7840 (pp) REVERT: C 274 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7962 (tppt) REVERT: C 426 GLU cc_start: 0.8071 (tp30) cc_final: 0.7700 (tp30) REVERT: C 498 LYS cc_start: 0.8606 (tttm) cc_final: 0.8350 (tttm) REVERT: C 596 LYS cc_start: 0.8556 (mttp) cc_final: 0.8224 (mttp) REVERT: C 672 GLN cc_start: 0.8255 (mt0) cc_final: 0.7992 (tp40) REVERT: C 676 GLU cc_start: 0.7823 (tp30) cc_final: 0.7385 (mp0) REVERT: C 763 TYR cc_start: 0.8414 (m-80) cc_final: 0.8194 (m-80) REVERT: C 819 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7722 (ttt90) REVERT: C 876 GLN cc_start: 0.7680 (tt0) cc_final: 0.7425 (tt0) REVERT: C 953 TYR cc_start: 0.8062 (m-80) cc_final: 0.7840 (m-80) REVERT: D 274 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7724 (mmmt) REVERT: D 374 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 386 LYS cc_start: 0.9154 (mtmm) cc_final: 0.7828 (tppt) REVERT: D 392 ASP cc_start: 0.7626 (t0) cc_final: 0.7301 (t0) REVERT: D 426 GLU cc_start: 0.8060 (tp30) cc_final: 0.7688 (tp30) REVERT: D 439 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7792 (m) REVERT: D 440 ASN cc_start: 0.7819 (m-40) cc_final: 0.7460 (m110) REVERT: D 763 TYR cc_start: 0.8436 (m-80) cc_final: 0.8213 (m-80) REVERT: D 784 TYR cc_start: 0.6658 (t80) cc_final: 0.6418 (t80) REVERT: D 1068 MET cc_start: 0.4771 (tpt) cc_final: 0.4500 (tpt) outliers start: 141 outliers final: 64 residues processed: 757 average time/residue: 1.0685 time to fit residues: 979.5864 Evaluate side-chains 669 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 601 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 244 optimal weight: 0.0060 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 82 optimal weight: 0.0470 overall best weight: 1.1698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 490 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 490 ASN D 297 GLN D 490 ASN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29236 Z= 0.268 Angle : 0.636 8.547 39516 Z= 0.326 Chirality : 0.043 0.184 4400 Planarity : 0.004 0.065 4816 Dihedral : 10.070 93.594 4256 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.34 % Allowed : 23.24 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3336 helix: 0.13 (0.11), residues: 2312 sheet: -1.98 (0.36), residues: 176 loop : -2.54 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 888 HIS 0.007 0.001 HIS B 176 PHE 0.015 0.001 PHE D 514 TYR 0.035 0.002 TYR A 286 ARG 0.006 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 635 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8504 (ttpt) cc_final: 0.7850 (mmmt) REVERT: A 374 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: A 426 GLU cc_start: 0.8098 (tp30) cc_final: 0.7710 (tp30) REVERT: A 518 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8289 (ptp) REVERT: A 971 TYR cc_start: 0.8687 (p90) cc_final: 0.8471 (p90) REVERT: A 995 TYR cc_start: 0.8108 (t80) cc_final: 0.7901 (t80) REVERT: B 274 LYS cc_start: 0.8573 (ttpt) cc_final: 0.7883 (mmmt) REVERT: B 426 GLU cc_start: 0.8107 (tp30) cc_final: 0.7696 (tp30) REVERT: B 876 GLN cc_start: 0.7701 (tt0) cc_final: 0.7401 (tt0) REVERT: B 1068 MET cc_start: 0.5795 (tpt) cc_final: 0.5504 (tpt) REVERT: C 274 LYS cc_start: 0.8568 (ttpt) cc_final: 0.7862 (mmmt) REVERT: C 392 ASP cc_start: 0.7619 (t0) cc_final: 0.7158 (t0) REVERT: C 426 GLU cc_start: 0.8124 (tp30) cc_final: 0.7731 (tp30) REVERT: C 498 LYS cc_start: 0.8636 (tttm) cc_final: 0.8413 (tttm) REVERT: C 569 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8442 (mttt) REVERT: C 596 LYS cc_start: 0.8593 (mttp) cc_final: 0.8286 (mttp) REVERT: C 676 GLU cc_start: 0.7824 (tp30) cc_final: 0.7414 (mp0) REVERT: C 780 ASN cc_start: 0.5242 (t0) cc_final: 0.4963 (m-40) REVERT: C 876 GLN cc_start: 0.7684 (tt0) cc_final: 0.7398 (tt0) REVERT: C 995 TYR cc_start: 0.8126 (t80) cc_final: 0.7918 (t80) REVERT: C 1068 MET cc_start: 0.5618 (tpt) cc_final: 0.5344 (tpt) REVERT: D 233 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: D 274 LYS cc_start: 0.8432 (ttpt) cc_final: 0.7798 (mmmt) REVERT: D 374 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: D 392 ASP cc_start: 0.7622 (t0) cc_final: 0.7399 (t0) REVERT: D 426 GLU cc_start: 0.8098 (tp30) cc_final: 0.7719 (tp30) REVERT: D 440 ASN cc_start: 0.7804 (m-40) cc_final: 0.7489 (m110) REVERT: D 763 TYR cc_start: 0.8462 (m-80) cc_final: 0.8259 (m-80) REVERT: D 1068 MET cc_start: 0.4713 (tpt) cc_final: 0.4513 (tpt) outliers start: 164 outliers final: 85 residues processed: 718 average time/residue: 1.1030 time to fit residues: 955.5900 Evaluate side-chains 687 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 598 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 3.9990 chunk 295 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 308 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 657 GLN C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 297 GLN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29236 Z= 0.372 Angle : 0.705 9.754 39516 Z= 0.357 Chirality : 0.045 0.170 4400 Planarity : 0.005 0.057 4816 Dihedral : 10.189 89.805 4256 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.24 % Allowed : 24.22 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3336 helix: 0.14 (0.11), residues: 2308 sheet: -1.89 (0.36), residues: 176 loop : -2.57 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 888 HIS 0.008 0.001 HIS C 176 PHE 0.017 0.002 PHE A 514 TYR 0.033 0.002 TYR C 763 ARG 0.012 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 640 time to evaluate : 3.237 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: A 374 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 386 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8110 (tppt) REVERT: A 426 GLU cc_start: 0.8193 (tp30) cc_final: 0.7774 (tp30) REVERT: A 518 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8268 (ptp) REVERT: A 971 TYR cc_start: 0.8738 (p90) cc_final: 0.8447 (p90) REVERT: B 164 GLN cc_start: 0.8395 (tp40) cc_final: 0.8158 (tp40) REVERT: B 274 LYS cc_start: 0.8660 (ttpt) cc_final: 0.7821 (mmmm) REVERT: B 426 GLU cc_start: 0.8188 (tp30) cc_final: 0.7791 (tp30) REVERT: B 876 GLN cc_start: 0.7759 (tt0) cc_final: 0.7436 (tt0) REVERT: B 995 TYR cc_start: 0.8136 (t80) cc_final: 0.7919 (t80) REVERT: B 1068 MET cc_start: 0.5481 (tpt) cc_final: 0.5189 (tpt) REVERT: C 274 LYS cc_start: 0.8638 (ttpt) cc_final: 0.7797 (mmmm) REVERT: C 386 LYS cc_start: 0.9170 (mtmm) cc_final: 0.7786 (tppt) REVERT: C 426 GLU cc_start: 0.8191 (tp30) cc_final: 0.7790 (tp30) REVERT: C 676 GLU cc_start: 0.7839 (tp30) cc_final: 0.7419 (mp0) REVERT: C 876 GLN cc_start: 0.7741 (tt0) cc_final: 0.7480 (tt0) REVERT: C 995 TYR cc_start: 0.8244 (t80) cc_final: 0.8044 (t80) REVERT: D 164 GLN cc_start: 0.8410 (tp40) cc_final: 0.8182 (tp40) REVERT: D 426 GLU cc_start: 0.8196 (tp30) cc_final: 0.7795 (tp30) REVERT: D 440 ASN cc_start: 0.7775 (m-40) cc_final: 0.7386 (m110) REVERT: D 995 TYR cc_start: 0.8213 (t80) cc_final: 0.7972 (t80) outliers start: 161 outliers final: 97 residues processed: 706 average time/residue: 1.0687 time to fit residues: 914.0205 Evaluate side-chains 700 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 601 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 0.0870 chunk 183 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN B 550 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN C 597 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN C 993 GLN D 297 GLN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 550 HIS ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 993 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29236 Z= 0.204 Angle : 0.644 10.286 39516 Z= 0.322 Chirality : 0.042 0.182 4400 Planarity : 0.004 0.054 4816 Dihedral : 9.363 89.539 4256 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.69 % Allowed : 25.65 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3336 helix: 0.47 (0.11), residues: 2312 sheet: -1.80 (0.36), residues: 176 loop : -2.35 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 888 HIS 0.007 0.001 HIS B 176 PHE 0.023 0.001 PHE C 989 TYR 0.027 0.001 TYR D 286 ARG 0.012 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 671 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 264 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.6991 (t) REVERT: A 274 LYS cc_start: 0.8537 (ttpt) cc_final: 0.7856 (mmtt) REVERT: A 374 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 386 LYS cc_start: 0.9119 (mtmm) cc_final: 0.7788 (tppt) REVERT: A 426 GLU cc_start: 0.8088 (tp30) cc_final: 0.7696 (tp30) REVERT: A 518 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8255 (ptp) REVERT: A 773 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: A 949 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 200 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8528 (p) REVERT: B 264 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7041 (t) REVERT: B 426 GLU cc_start: 0.8105 (tp30) cc_final: 0.7719 (tp30) REVERT: B 762 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7043 (mp) REVERT: B 949 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 1068 MET cc_start: 0.5527 (tpt) cc_final: 0.5310 (tpt) REVERT: C 179 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8393 (tp) REVERT: C 264 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6971 (t) REVERT: C 386 LYS cc_start: 0.8986 (mtmm) cc_final: 0.7668 (tppt) REVERT: C 426 GLU cc_start: 0.8112 (tp30) cc_final: 0.7723 (tp30) REVERT: C 676 GLU cc_start: 0.7822 (tp30) cc_final: 0.7431 (mp0) REVERT: C 780 ASN cc_start: 0.5509 (t0) cc_final: 0.5022 (m-40) REVERT: C 1068 MET cc_start: 0.5504 (tpt) cc_final: 0.5284 (tpt) REVERT: D 264 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7072 (t) REVERT: D 274 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7921 (mmtt) REVERT: D 426 GLU cc_start: 0.8118 (tp30) cc_final: 0.7730 (tp30) REVERT: D 440 ASN cc_start: 0.7791 (m-40) cc_final: 0.7436 (m110) REVERT: D 1068 MET cc_start: 0.5574 (tpt) cc_final: 0.5322 (tpt) outliers start: 144 outliers final: 75 residues processed: 743 average time/residue: 1.0999 time to fit residues: 987.1507 Evaluate side-chains 697 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 609 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 646 ASN Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 308 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29236 Z= 0.216 Angle : 0.655 10.120 39516 Z= 0.329 Chirality : 0.042 0.192 4400 Planarity : 0.004 0.057 4816 Dihedral : 9.066 89.102 4256 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.43 % Allowed : 26.40 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3336 helix: 0.63 (0.11), residues: 2288 sheet: -1.68 (0.37), residues: 176 loop : -2.25 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 888 HIS 0.006 0.001 HIS B 176 PHE 0.016 0.001 PHE B 146 TYR 0.034 0.002 TYR D 763 ARG 0.013 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 666 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7358 (mtm) REVERT: A 264 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.7030 (t) REVERT: A 274 LYS cc_start: 0.8515 (ttpt) cc_final: 0.7856 (mmtt) REVERT: A 374 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 386 LYS cc_start: 0.8978 (mtmm) cc_final: 0.7797 (tppt) REVERT: A 426 GLU cc_start: 0.8073 (tp30) cc_final: 0.7688 (tp30) REVERT: A 518 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8265 (ptp) REVERT: A 753 LYS cc_start: 0.7366 (tppp) cc_final: 0.7100 (tptp) REVERT: A 853 MET cc_start: 0.8633 (mtt) cc_final: 0.8292 (mtt) REVERT: A 949 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 274 LYS cc_start: 0.8616 (ttpt) cc_final: 0.7951 (mmtt) REVERT: B 426 GLU cc_start: 0.8101 (tp30) cc_final: 0.7727 (tp30) REVERT: B 753 LYS cc_start: 0.7481 (tptm) cc_final: 0.7271 (tptp) REVERT: B 995 TYR cc_start: 0.7869 (t80) cc_final: 0.7633 (t80) REVERT: B 1068 MET cc_start: 0.5594 (tpt) cc_final: 0.5113 (tpt) REVERT: C 274 LYS cc_start: 0.8502 (ttpt) cc_final: 0.7875 (mmtt) REVERT: C 426 GLU cc_start: 0.8121 (tp30) cc_final: 0.7734 (tp30) REVERT: C 762 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6943 (mp) REVERT: C 763 TYR cc_start: 0.7073 (m-80) cc_final: 0.6817 (m-80) REVERT: C 1068 MET cc_start: 0.5638 (tpt) cc_final: 0.5295 (tpt) REVERT: D 274 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7925 (mmtt) REVERT: D 426 GLU cc_start: 0.8123 (tp30) cc_final: 0.7737 (tp30) REVERT: D 440 ASN cc_start: 0.7704 (m-40) cc_final: 0.7360 (m110) outliers start: 136 outliers final: 78 residues processed: 725 average time/residue: 1.0934 time to fit residues: 963.6763 Evaluate side-chains 688 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 604 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 854 MET Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 275 optimal weight: 5.9990 chunk 288 optimal weight: 0.5980 chunk 304 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 490 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29236 Z= 0.208 Angle : 0.662 10.667 39516 Z= 0.329 Chirality : 0.042 0.192 4400 Planarity : 0.004 0.057 4816 Dihedral : 8.777 89.063 4256 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.61 % Allowed : 28.03 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3336 helix: 0.79 (0.11), residues: 2284 sheet: -1.65 (0.37), residues: 176 loop : -2.24 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 888 HIS 0.006 0.001 HIS A 176 PHE 0.017 0.001 PHE D 969 TYR 0.031 0.002 TYR D 763 ARG 0.014 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 658 time to evaluate : 3.249 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: A 164 GLN cc_start: 0.8465 (tp40) cc_final: 0.8180 (tp40) REVERT: A 274 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7781 (mmmt) REVERT: A 374 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 386 LYS cc_start: 0.8873 (mtmm) cc_final: 0.7590 (tppt) REVERT: A 426 GLU cc_start: 0.8087 (tp30) cc_final: 0.7691 (tp30) REVERT: A 853 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8245 (mtt) REVERT: A 949 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 1068 MET cc_start: 0.6028 (tpt) cc_final: 0.5679 (tpp) REVERT: B 179 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 203 ILE cc_start: 0.8973 (mt) cc_final: 0.8729 (mm) REVERT: B 274 LYS cc_start: 0.8535 (ttpt) cc_final: 0.7877 (mmtt) REVERT: B 426 GLU cc_start: 0.8055 (tp30) cc_final: 0.7680 (tp30) REVERT: B 436 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: B 949 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 995 TYR cc_start: 0.7934 (t80) cc_final: 0.7696 (t80) REVERT: B 1068 MET cc_start: 0.5604 (tpt) cc_final: 0.5307 (tpt) REVERT: C 179 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 426 GLU cc_start: 0.8101 (tp30) cc_final: 0.7721 (tp30) REVERT: C 1005 PHE cc_start: 0.7698 (m-10) cc_final: 0.7422 (m-80) REVERT: C 1068 MET cc_start: 0.5645 (tpt) cc_final: 0.5353 (tpt) REVERT: D 203 ILE cc_start: 0.8969 (mt) cc_final: 0.8741 (mm) REVERT: D 274 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7874 (mmmt) REVERT: D 426 GLU cc_start: 0.8101 (tp30) cc_final: 0.7726 (tp30) REVERT: D 440 ASN cc_start: 0.7601 (m-40) cc_final: 0.7237 (m110) REVERT: D 1005 PHE cc_start: 0.7715 (m-10) cc_final: 0.7395 (m-80) outliers start: 111 outliers final: 69 residues processed: 705 average time/residue: 1.0821 time to fit residues: 925.1192 Evaluate side-chains 688 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 612 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 854 MET Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 311 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29236 Z= 0.274 Angle : 0.710 13.086 39516 Z= 0.353 Chirality : 0.044 0.194 4400 Planarity : 0.004 0.055 4816 Dihedral : 8.877 89.166 4256 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.22 % Allowed : 29.43 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3336 helix: 0.74 (0.11), residues: 2284 sheet: -1.63 (0.38), residues: 176 loop : -2.25 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 888 HIS 0.008 0.001 HIS D 176 PHE 0.019 0.001 PHE B 969 TYR 0.038 0.002 TYR D 763 ARG 0.014 0.000 ARG B 998 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 624 time to evaluate : 3.217 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: A 164 GLN cc_start: 0.8451 (tp40) cc_final: 0.8179 (tp40) REVERT: A 274 LYS cc_start: 0.8508 (ttpt) cc_final: 0.7880 (mmpt) REVERT: A 374 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 386 LYS cc_start: 0.8990 (mtmm) cc_final: 0.7638 (tppt) REVERT: A 426 GLU cc_start: 0.8105 (tp30) cc_final: 0.7703 (tp30) REVERT: A 773 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 853 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: A 1068 MET cc_start: 0.6214 (tpt) cc_final: 0.5920 (tpp) REVERT: B 203 ILE cc_start: 0.9013 (mt) cc_final: 0.8789 (mm) REVERT: B 274 LYS cc_start: 0.8529 (ttpt) cc_final: 0.7883 (mmtt) REVERT: B 426 GLU cc_start: 0.8113 (tp30) cc_final: 0.7737 (tp30) REVERT: B 436 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8260 (mm-30) REVERT: B 1068 MET cc_start: 0.5534 (tpt) cc_final: 0.5232 (tpt) REVERT: C 179 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (tp) REVERT: C 426 GLU cc_start: 0.8151 (tp30) cc_final: 0.7760 (tp30) REVERT: C 1068 MET cc_start: 0.5784 (tpt) cc_final: 0.5492 (tpt) REVERT: D 203 ILE cc_start: 0.8991 (mt) cc_final: 0.8737 (mm) REVERT: D 426 GLU cc_start: 0.8151 (tp30) cc_final: 0.7767 (tp30) REVERT: D 440 ASN cc_start: 0.7597 (m-40) cc_final: 0.7223 (m110) REVERT: D 1068 MET cc_start: 0.6178 (tpt) cc_final: 0.5864 (tpp) outliers start: 99 outliers final: 71 residues processed: 661 average time/residue: 1.1039 time to fit residues: 886.0803 Evaluate side-chains 676 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 601 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 853 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 853 MET Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 853 MET Chi-restraints excluded: chain D residue 854 MET Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 277 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 672 GLN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130710 restraints weight = 36174.619| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.34 r_work: 0.3341 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29236 Z= 0.213 Angle : 0.698 14.637 39516 Z= 0.342 Chirality : 0.043 0.197 4400 Planarity : 0.004 0.062 4816 Dihedral : 8.602 89.643 4256 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.35 % Allowed : 29.85 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3336 helix: 0.86 (0.11), residues: 2284 sheet: -1.64 (0.38), residues: 176 loop : -2.24 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 888 HIS 0.005 0.001 HIS A 176 PHE 0.020 0.001 PHE C 969 TYR 0.033 0.002 TYR D 763 ARG 0.016 0.000 ARG B 998 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13059.80 seconds wall clock time: 230 minutes 14.27 seconds (13814.27 seconds total)