Starting phenix.real_space_refine on Thu Dec 14 18:01:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvi_34128/12_2023/7yvi_34128.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18479 2.51 5 N 4774 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "O ARG 87": "NH1" <-> "NH2" Residue "O ARG 98": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28961 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.42, per 1000 atoms: 0.53 Number of scatterers: 28961 At special positions: 0 Unit cell: (171.38, 147.6, 201.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5579 8.00 N 4774 7.00 C 18479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.88 Conformation dependent library (CDL) restraints added in 4.8 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 20.5% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.503A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.432A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.702A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.833A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.690A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.348A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.996A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.540A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.902A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.802A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.146A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.831A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.515A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.639A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.780A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.972A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.600A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.188A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.988A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASP J 31 " --> pdb=" O MET J 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.729A pdb=" N THR J 91 " --> pdb=" O VAL J 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.623A pdb=" N ASP O 31 " --> pdb=" O MET O 28 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 28 through 32' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR O 91 " --> pdb=" O VAL O 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.057A pdb=" N ASP K 31 " --> pdb=" O MET K 28 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.543A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.535A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.169A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.556A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.517A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.267A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.570A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.514A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.990A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.566A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.445A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.030A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.281A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.075A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.339A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.452A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.892A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.566A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.144A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.662A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.873A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.195A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.258A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.981A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.815A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.694A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR J 80 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.480A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR J 59 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER N 92 " --> pdb=" O VAL N 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.061A pdb=" N SER O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.904A pdb=" N MET K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3009 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: 13.59 Time building geometry restraints manager: 11.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7874 1.33 - 1.47: 10469 1.47 - 1.60: 11131 1.60 - 1.74: 34 1.74 - 1.88: 131 Bond restraints: 29639 Sorted by residual: bond pdb=" CA THR C1066 " pdb=" CB THR C1066 " ideal model delta sigma weight residual 1.534 1.404 0.130 2.33e-02 1.84e+03 3.11e+01 bond pdb=" CB ASN B 907 " pdb=" CG ASN B 907 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.97e+01 bond pdb=" CA THR B1066 " pdb=" CB THR B1066 " ideal model delta sigma weight residual 1.534 1.415 0.120 2.33e-02 1.84e+03 2.65e+01 bond pdb=" CB ILE C 714 " pdb=" CG2 ILE C 714 " ideal model delta sigma weight residual 1.521 1.357 0.164 3.30e-02 9.18e+02 2.48e+01 bond pdb=" CB THR A1077 " pdb=" CG2 THR A1077 " ideal model delta sigma weight residual 1.521 1.358 0.163 3.30e-02 9.18e+02 2.43e+01 ... (remaining 29634 not shown) Histogram of bond angle deviations from ideal: 91.74 - 100.30: 42 100.30 - 108.85: 4243 108.85 - 117.40: 17175 117.40 - 125.96: 18580 125.96 - 134.51: 407 Bond angle restraints: 40447 Sorted by residual: angle pdb=" N GLY A 416 " pdb=" CA GLY A 416 " pdb=" C GLY A 416 " ideal model delta sigma weight residual 113.18 96.12 17.06 2.37e+00 1.78e-01 5.18e+01 angle pdb=" CA CYS A 649 " pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 114.40 129.17 -14.77 2.30e+00 1.89e-01 4.12e+01 angle pdb=" CB LEU B 878 " pdb=" CG LEU B 878 " pdb=" CD2 LEU B 878 " ideal model delta sigma weight residual 110.70 91.74 18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C PHE C 565 " pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " ideal model delta sigma weight residual 109.79 97.14 12.65 2.05e+00 2.38e-01 3.81e+01 angle pdb=" CA CYS C 538 " pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " ideal model delta sigma weight residual 114.40 128.43 -14.03 2.30e+00 1.89e-01 3.72e+01 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 16323 17.69 - 35.38: 1288 35.38 - 53.07: 262 53.07 - 70.76: 63 70.76 - 88.44: 22 Dihedral angle restraints: 17958 sinusoidal: 7026 harmonic: 10932 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.84 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.04 -76.96 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.98 -74.02 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3526 0.103 - 0.206: 988 0.206 - 0.309: 147 0.309 - 0.412: 21 0.412 - 0.515: 5 Chirality restraints: 4687 Sorted by residual: chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB VAL B1094 " pdb=" CA VAL B1094 " pdb=" CG1 VAL B1094 " pdb=" CG2 VAL B1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 4684 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 67 " -0.074 9.50e-02 1.11e+02 5.93e-02 3.09e+01 pdb=" NE ARG J 67 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG J 67 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG J 67 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG J 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 115 " -0.021 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP O 115 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP O 115 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP O 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP O 115 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP O 115 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 115 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 115 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP O 115 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 374 " 0.049 2.00e-02 2.50e+03 3.68e-02 2.36e+01 pdb=" CG PHE B 374 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE B 374 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 374 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 374 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 374 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 374 " 0.017 2.00e-02 2.50e+03 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 716 2.60 - 3.18: 26798 3.18 - 3.75: 41826 3.75 - 4.33: 55046 4.33 - 4.90: 94985 Nonbonded interactions: 219371 Sorted by model distance: nonbonded pdb=" OG SER O 7 " pdb=" OG SER O 21 " model vdw 2.028 2.440 nonbonded pdb=" O LYS C 440 " pdb=" OH TYR I 32 " model vdw 2.032 2.440 nonbonded pdb=" OD2 ASP B 737 " pdb=" ND2 ASN A 317 " model vdw 2.036 2.520 nonbonded pdb=" NH1 ARG N 63 " pdb=" O GLY N 79 " model vdw 2.051 2.520 nonbonded pdb=" ND2 ASN A1134 " pdb=" O7 NAG A1308 " model vdw 2.053 2.520 ... (remaining 219366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1312)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.930 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: 28.890 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 76.780 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.026 0.195 29639 Z= 1.721 Angle : 1.685 18.957 40447 Z= 0.923 Chirality : 0.095 0.515 4687 Planarity : 0.009 0.114 5188 Dihedral : 13.427 88.444 10827 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.33 % Favored : 94.05 % Rotamer: Outliers : 1.33 % Allowed : 9.18 % Favored : 89.49 % Cbeta Deviations : 0.06 % 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: -2.56 (0.12), residues: 3717 helix: 0.08 (0.20), residues: 634 sheet: -1.46 (0.14), residues: 987 loop : -2.47 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.007 TRP O 115 HIS 0.025 0.005 HIS C1048 PHE 0.080 0.008 PHE B 374 TYR 0.059 0.005 TYR B 674 ARG 0.095 0.003 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 292 average time/residue: 0.4246 time to fit residues: 195.4228 Evaluate side-chains 198 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 2.944 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2680 time to fit residues: 10.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 20.0000 chunk 284 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 657 ASN C 755 GLN C1098 ASN B 188 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN B 755 GLN B 762 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN A 165 ASN A 234 ASN A 370 ASN A 437 ASN A 505 HIS A 540 ASN A 657 ASN A 801 ASN A 965 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 39 GLN N 39 GLN O 74 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29639 Z= 0.233 Angle : 0.663 11.331 40447 Z= 0.349 Chirality : 0.047 0.236 4687 Planarity : 0.005 0.058 5188 Dihedral : 6.630 54.420 4827 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 2.33 % Allowed : 12.51 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.61 (0.13), residues: 3717 helix: 1.31 (0.21), residues: 635 sheet: -0.89 (0.14), residues: 1093 loop : -2.04 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.005 0.001 HIS B1088 PHE 0.019 0.002 PHE A 238 TYR 0.022 0.002 TYR B 265 ARG 0.004 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 26 residues processed: 322 average time/residue: 0.3865 time to fit residues: 205.3582 Evaluate side-chains 242 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.854 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2618 time to fit residues: 17.4179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 283 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 368 optimal weight: 8.9990 chunk 303 optimal weight: 0.8980 chunk 338 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 273 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1074 ASN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN N 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29639 Z= 0.224 Angle : 0.616 15.141 40447 Z= 0.320 Chirality : 0.045 0.314 4687 Planarity : 0.004 0.041 5188 Dihedral : 5.849 55.820 4827 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.83 % Rotamer: Outliers : 2.36 % Allowed : 15.40 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.13), residues: 3717 helix: 1.78 (0.21), residues: 645 sheet: -0.49 (0.15), residues: 1100 loop : -1.74 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.018 0.001 PHE C 201 TYR 0.022 0.001 TYR N 93 ARG 0.003 0.000 ARG O 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 232 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 36 residues processed: 291 average time/residue: 0.4038 time to fit residues: 194.3978 Evaluate side-chains 239 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 3.136 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2677 time to fit residues: 22.2644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 177 optimal weight: 0.5980 chunk 37 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 50.0000 chunk 178 optimal weight: 0.6980 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN J 82 GLN N 39 GLN N 41 HIS O 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29639 Z= 0.249 Angle : 0.606 16.856 40447 Z= 0.315 Chirality : 0.045 0.342 4687 Planarity : 0.004 0.048 5188 Dihedral : 5.627 56.999 4827 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 2.33 % Allowed : 16.10 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.87 (0.13), residues: 3717 helix: 1.93 (0.21), residues: 635 sheet: -0.31 (0.15), residues: 1085 loop : -1.62 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 37 HIS 0.004 0.001 HIS A1064 PHE 0.023 0.001 PHE C 168 TYR 0.021 0.001 TYR B 170 ARG 0.005 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 219 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 274 average time/residue: 0.3960 time to fit residues: 179.8116 Evaluate side-chains 234 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2702 time to fit residues: 19.6775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.5980 chunk 205 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 0.1980 chunk 325 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 751 ASN B 762 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 992 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN N 41 HIS O 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29639 Z= 0.351 Angle : 0.654 17.249 40447 Z= 0.340 Chirality : 0.047 0.407 4687 Planarity : 0.004 0.048 5188 Dihedral : 5.682 57.215 4827 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.05 % Rotamer: Outliers : 2.30 % Allowed : 17.90 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.84 (0.13), residues: 3717 helix: 1.77 (0.21), residues: 634 sheet: -0.18 (0.16), residues: 1003 loop : -1.55 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.006 0.001 HIS A1064 PHE 0.024 0.002 PHE C 238 TYR 0.026 0.002 TYR A1067 ARG 0.010 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 210 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 35 residues processed: 269 average time/residue: 0.4093 time to fit residues: 182.0220 Evaluate side-chains 227 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2753 time to fit residues: 22.4748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 40.0000 chunk 326 optimal weight: 40.0000 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 362 optimal weight: 30.0000 chunk 301 optimal weight: 0.0070 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 41 HIS O 77 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29639 Z= 0.235 Angle : 0.591 15.861 40447 Z= 0.308 Chirality : 0.045 0.334 4687 Planarity : 0.004 0.053 5188 Dihedral : 5.372 54.615 4827 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.52 % Favored : 94.35 % Rotamer: Outliers : 1.63 % Allowed : 19.10 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.67 (0.13), residues: 3717 helix: 2.02 (0.21), residues: 634 sheet: -0.11 (0.16), residues: 967 loop : -1.44 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B1088 PHE 0.019 0.001 PHE C 201 TYR 0.024 0.001 TYR N 93 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 249 average time/residue: 0.3973 time to fit residues: 163.7335 Evaluate side-chains 226 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 3.433 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2677 time to fit residues: 16.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 305 optimal weight: 0.1980 chunk 202 optimal weight: 0.7980 chunk 361 optimal weight: 40.0000 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 0.4980 chunk 166 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS N 81 GLN O 77 ASN I 55 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29639 Z= 0.169 Angle : 0.567 19.972 40447 Z= 0.294 Chirality : 0.044 0.400 4687 Planarity : 0.004 0.051 5188 Dihedral : 5.012 59.135 4827 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 1.03 % Allowed : 19.49 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3717 helix: 2.34 (0.21), residues: 627 sheet: 0.07 (0.16), residues: 984 loop : -1.30 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.003 0.000 HIS C 69 PHE 0.035 0.001 PHE O 78 TYR 0.022 0.001 TYR N 93 ARG 0.010 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 4.239 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 9 residues processed: 247 average time/residue: 0.4252 time to fit residues: 174.9602 Evaluate side-chains 216 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3071 time to fit residues: 9.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 229 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29639 Z= 0.206 Angle : 0.570 13.612 40447 Z= 0.295 Chirality : 0.044 0.361 4687 Planarity : 0.004 0.053 5188 Dihedral : 4.939 59.733 4827 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 0.86 % Allowed : 20.16 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.14), residues: 3717 helix: 2.33 (0.21), residues: 630 sheet: 0.15 (0.16), residues: 965 loop : -1.26 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 PHE 0.021 0.001 PHE O 68 TYR 0.023 0.001 TYR B 170 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 222 average time/residue: 0.3810 time to fit residues: 142.7888 Evaluate side-chains 212 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 3.125 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2673 time to fit residues: 12.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 336 optimal weight: 30.0000 chunk 202 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 318 optimal weight: 0.0570 chunk 335 optimal weight: 7.9990 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29639 Z= 0.302 Angle : 0.612 17.172 40447 Z= 0.318 Chirality : 0.045 0.351 4687 Planarity : 0.004 0.050 5188 Dihedral : 5.133 57.609 4827 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.78 % Favored : 94.11 % Rotamer: Outliers : 0.57 % Allowed : 20.16 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.44 (0.13), residues: 3717 helix: 2.09 (0.21), residues: 629 sheet: 0.05 (0.16), residues: 977 loop : -1.25 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 PHE 0.032 0.002 PHE O 78 TYR 0.025 0.001 TYR A1067 ARG 0.007 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 218 average time/residue: 0.3842 time to fit residues: 140.9094 Evaluate side-chains 205 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 3.018 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3132 time to fit residues: 8.5748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 3.9990 chunk 356 optimal weight: 50.0000 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 182 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 317 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29639 Z= 0.304 Angle : 0.616 16.077 40447 Z= 0.320 Chirality : 0.045 0.335 4687 Planarity : 0.004 0.052 5188 Dihedral : 5.203 56.291 4827 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 0.63 % Allowed : 20.16 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.14), residues: 3717 helix: 2.04 (0.21), residues: 629 sheet: 0.10 (0.16), residues: 1000 loop : -1.24 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 PHE 0.032 0.002 PHE C 238 TYR 0.026 0.001 TYR N 93 ARG 0.006 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 205 average time/residue: 0.3985 time to fit residues: 138.2073 Evaluate side-chains 202 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2635 time to fit residues: 10.4481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 6.9990 chunk 316 optimal weight: 40.0000 chunk 91 optimal weight: 0.5980 chunk 274 optimal weight: 0.0570 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.177137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103686 restraints weight = 49536.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108100 restraints weight = 26922.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108777 restraints weight = 15504.004| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29639 Z= 0.232 Angle : 0.586 15.458 40447 Z= 0.302 Chirality : 0.044 0.319 4687 Planarity : 0.004 0.050 5188 Dihedral : 5.041 57.358 4827 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 0.20 % Allowed : 20.43 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.31 (0.14), residues: 3717 helix: 2.17 (0.21), residues: 629 sheet: 0.18 (0.16), residues: 992 loop : -1.19 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 PHE 0.030 0.001 PHE C 238 TYR 0.024 0.001 TYR N 93 ARG 0.006 0.000 ARG C 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.67 seconds wall clock time: 99 minutes 6.07 seconds (5946.07 seconds total)