Starting phenix.real_space_refine on Sat Feb 17 14:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/02_2024/6olp_20118_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 116 5.16 5 C 11840 2.51 5 N 3064 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 557": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18868 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1152 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3454 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 22, 'TRANS': 396} Chain breaks: 6 Chain: "F" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1063 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 2 Chain: "G" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1062 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "I" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 393 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 393 " occ=0.50 Time building chain proxies: 13.15, per 1000 atoms: 0.70 Number of scatterers: 18868 At special positions: 0 Unit cell: (127.72, 133.9, 147.29, 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 116 16.00 O 3848 8.00 N 3064 7.00 C 11840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 7 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 9 " ALPHA1-6 " BMA V 3 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN e 4 " - " NAG e 5 " " MAN e 7 " - " NAG e 8 " " MAN f 4 " - " NAG f 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " MAN V 4 " - " NAG V 7 " " NAG V 5 " - " GAL V 6 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG W 5 " - " GAL W 6 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG e 5 " - " GAL e 6 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " BETA1-6 " NAG K 1 " - " NAG K 2 " " NAG V 1 " - " FUC V 9 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 8 " " MAN W 4 " - " NAG W 5 " " NAG X 1 " - " FUC X 2 " " NAG c 1 " - " FUC c 2 " " NAG e 1 " - " FUC e 9 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 618 " - " ASN A 332 " " NAG A 619 " - " ASN A 392 " " NAG A 629 " - " ASN A 188 " " NAG A 632 " - " ASN A 356 " " NAG A 633 " - " ASN A 362 " " NAG C 603 " - " ASN C 130 " " NAG C 606 " - " ASN C 234 " " NAG C 614 " - " ASN C 448 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 156 " " NAG C 617 " - " ASN C 188 " " NAG C 620 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 622 " - " ASN C 332 " " NAG C 623 " - " ASN C 289 " " NAG C 624 " - " ASN C 392 " " NAG C 627 " - " ASN C 356 " " NAG C 628 " - " ASN C 362 " " NAG D 901 " - " ASN D 625 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 156 " " NAG E 610 " - " ASN E 276 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 332 " " NAG E 613 " - " ASN E 295 " " NAG E 614 " - " ASN E 301 " " NAG E 615 " - " ASN E 392 " " NAG E 616 " - " ASN E 362 " " NAG E 617 " - " ASN E 234 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 188 " " NAG E 620 " - " ASN E 197 " " NAG E 621 " - " ASN E 130 " " NAG E 622 " - " ASN E 448 " " NAG F 901 " - " ASN F 616 " " NAG F 902 " - " ASN F 625 " " NAG F 903 " - " ASN F 637 " " NAG F 904 " - " ASN F 611 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 241 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 289 " " NAG V 1 " - " ASN B 637 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN B 625 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 197 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN D 637 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 241 " " NAG i 1 " - " ASN E 262 " Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 4.0 seconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 37 sheets defined 16.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.797A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.119A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.704A pdb=" N ASN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.524A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 538 removed outlier: 3.921A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.541A pdb=" N VAL B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN B 550 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 552 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN B 553 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 555 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.091A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.530A pdb=" N TRP B 623 " --> pdb=" O TYR B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 623' Processing helix chain 'B' and resid 629 through 635 removed outlier: 3.519A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 647 removed outlier: 3.648A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 663 Processing helix chain 'C' and resid 100 through 117 removed outlier: 3.523A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.291A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'D' and resid 530 through 533 No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 573 through 595 removed outlier: 4.283A pdb=" N GLN D 577 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL D 580 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA D 582 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 585 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 587 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 588 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 589 " --> pdb=" O TYR D 586 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 592 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 595 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.886A pdb=" N ARG D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 removed outlier: 4.354A pdb=" N SER D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR D 644 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.118A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.514A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 105' Processing helix chain 'E' and resid 108 through 114 removed outlier: 3.707A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.114A pdb=" N ASN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 340 " --> pdb=" O THR E 336 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 391 No H-bonds generated for 'chain 'E' and resid 388 through 391' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.581A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.575A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 533 through 544 removed outlier: 3.701A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN F 540 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 542 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU F 543 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 544 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 removed outlier: 4.169A pdb=" N ALA F 578 " --> pdb=" O ILE F 573 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG F 579 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 635 removed outlier: 3.526A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.514A pdb=" N THR F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 657 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= D, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.216A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.838A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.646A pdb=" N THR A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 443 through 449 removed outlier: 4.010A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 377 Processing sheet with id= I, first strand: chain 'A' and resid 303 through 308 removed outlier: 5.148A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= K, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 271 through 273 Processing sheet with id= M, first strand: chain 'C' and resid 443 through 447 removed outlier: 3.686A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 374 through 377 Processing sheet with id= O, first strand: chain 'C' and resid 307 through 312 removed outlier: 3.977A pdb=" N PHE C 317 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'E' and resid 53 through 56 removed outlier: 4.038A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= S, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.546A pdb=" N PHE E 176 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.979A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 486 through 490 removed outlier: 3.753A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 284 through 287 removed outlier: 6.802A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 331 through 333 Processing sheet with id= Y, first strand: chain 'E' and resid 304 through 308 Processing sheet with id= Z, first strand: chain 'E' and resid 374 through 377 Processing sheet with id= AA, first strand: chain 'G' and resid 10 through 12 Processing sheet with id= AB, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.400A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G 97 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL G 124 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 69 through 73 removed outlier: 3.728A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.654A pdb=" N SER I 22 " --> pdb=" O THR I 7 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.884A pdb=" N LYS I 103 " --> pdb=" O LEU I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'I' and resid 87 through 90 removed outlier: 6.113A pdb=" N ARG I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU I 46 " --> pdb=" O ARG I 37 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.606A pdb=" N VAL H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.722A pdb=" N THR H 132 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 131 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 92 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA H 97 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 97 through 99 removed outlier: 4.075A pdb=" N VAL H 124 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.579A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 85 through 87 removed outlier: 5.953A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 825 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: 5.18 Time building geometry restraints manager: 10.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5740 1.34 - 1.46: 4898 1.46 - 1.59: 8425 1.59 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 19228 Sorted by residual: bond pdb=" C ASP I 93 " pdb=" N PHE I 94 " ideal model delta sigma weight residual 1.331 1.222 0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C1 NAG C 615 " pdb=" O5 NAG C 615 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 MAN b 4 " pdb=" C2 MAN b 4 " ideal model delta sigma weight residual 1.526 1.597 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.418 1.480 -0.062 2.00e-02 2.50e+03 9.48e+00 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.49: 379 105.49 - 112.68: 10865 112.68 - 119.87: 6274 119.87 - 127.05: 8307 127.05 - 134.24: 265 Bond angle restraints: 26090 Sorted by residual: angle pdb=" C LEU B 565 " pdb=" N LEU B 566 " pdb=" CA LEU B 566 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C GLY A 354 " pdb=" N ASN A 356 " pdb=" CA ASN A 356 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C PHE C 353 " pdb=" N GLY C 354 " pdb=" CA GLY C 354 " ideal model delta sigma weight residual 121.41 131.10 -9.69 1.96e+00 2.60e-01 2.45e+01 angle pdb=" C PHE A 159 " pdb=" N ASN A 160 " pdb=" CA ASN A 160 " ideal model delta sigma weight residual 122.14 114.50 7.64 1.67e+00 3.59e-01 2.09e+01 angle pdb=" N ASN E 289 " pdb=" CA ASN E 289 " pdb=" C ASN E 289 " ideal model delta sigma weight residual 110.55 104.40 6.15 1.35e+00 5.49e-01 2.07e+01 ... (remaining 26085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 12467 23.48 - 46.95: 452 46.95 - 70.43: 121 70.43 - 93.90: 54 93.90 - 117.38: 49 Dihedral angle restraints: 13143 sinusoidal: 6852 harmonic: 6291 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -148.37 62.37 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 152.37 -59.37 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -137.52 51.52 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 13140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3243 0.160 - 0.321: 52 0.321 - 0.481: 9 0.481 - 0.641: 2 0.641 - 0.801: 2 Chirality restraints: 3308 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 625 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG C 623 " pdb=" ND2 ASN C 289 " pdb=" C2 NAG C 623 " pdb=" O5 NAG C 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3305 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN A 88 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 625 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ASN B 625 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN B 625 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 626 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 651 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" CG ASN B 651 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 651 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 651 " 0.017 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3125 2.76 - 3.29: 17477 3.29 - 3.83: 30855 3.83 - 4.36: 34448 4.36 - 4.90: 57857 Nonbonded interactions: 143762 Sorted by model distance: nonbonded pdb=" OG SER A 209 " pdb=" OE1 GLU A 211 " model vdw 2.224 2.440 nonbonded pdb=" OG SER I 25 " pdb=" O GLU I 27 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR A 303 " pdb=" O GLU A 322 " model vdw 2.263 2.440 nonbonded pdb=" OG SER G 120 " pdb=" OH TYR I 34 " model vdw 2.268 2.440 nonbonded pdb=" O MET H 122 " pdb=" OH TYR L 36 " model vdw 2.286 2.440 ... (remaining 143757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 392 or resid 413 through 457 \ or resid 467 through 505 or resid 603 through 633)) selection = (chain 'C' and (resid 33 through 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 364 or resid 368 through 392 \ or resid 413 through 457 or resid 467 through 505 or resid 617 through 628)) selection = (chain 'E' and (resid 33 through 134 or resid 152 through 364 or resid 368 throu \ gh 392 or resid 413 through 505 or resid 615 through 622)) } ncs_group { reference = (chain 'B' and (resid 522 through 557 or resid 571 through 574 or resid 576 thro \ ugh 659)) selection = (chain 'F' and resid 522 through 659) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 135) } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 2 through 105) } ncs_group { reference = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) } ncs_group { reference = chain 'R' selection = chain 'i' } ncs_group { reference = (chain 'V' and resid 9) selection = (chain 'W' and resid 8) selection = (chain 'e' and resid 9) selection = (chain 'f' and resid 10) } 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=0.50 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: 2.120 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: 12.870 Check model and map are aligned: 0.550 Set scattering table: 0.170 Process input model: 54.930 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 19228 Z= 0.555 Angle : 1.131 12.307 26090 Z= 0.558 Chirality : 0.070 0.801 3308 Planarity : 0.007 0.059 3132 Dihedral : 15.438 117.378 8979 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.57 % Allowed : 3.22 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.54 (0.15), residues: 2131 helix: -3.53 (0.18), residues: 342 sheet: -2.65 (0.19), residues: 537 loop : -3.12 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP F 614 HIS 0.012 0.002 HIS E 363 PHE 0.030 0.004 PHE I 49 TYR 0.036 0.003 TYR A 217 ARG 0.009 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 377 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8308 (m-90) cc_final: 0.7981 (m-90) REVERT: A 106 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7836 (pt0) REVERT: A 211 GLU cc_start: 0.8395 (mp0) cc_final: 0.8163 (mp0) REVERT: A 434 MET cc_start: 0.8873 (tmm) cc_final: 0.8474 (tmm) REVERT: B 638 TYR cc_start: 0.8994 (m-80) cc_final: 0.8764 (m-10) REVERT: B 645 LEU cc_start: 0.9481 (mt) cc_final: 0.9030 (tp) REVERT: B 656 ASN cc_start: 0.8931 (t0) cc_final: 0.8727 (t0) REVERT: B 657 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8823 (tm-30) REVERT: B 659 GLU cc_start: 0.9474 (tt0) cc_final: 0.9102 (tm-30) REVERT: C 42 VAL cc_start: 0.9409 (t) cc_final: 0.9149 (p) REVERT: C 260 LEU cc_start: 0.8864 (pp) cc_final: 0.8583 (pp) REVERT: C 304 ARG cc_start: 0.8363 (tpm170) cc_final: 0.8149 (mmm160) REVERT: D 626 MET cc_start: 0.8925 (mtp) cc_final: 0.8543 (ttm) REVERT: D 632 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8213 (tm-30) REVERT: D 651 ASN cc_start: 0.8850 (m-40) cc_final: 0.8618 (t0) REVERT: E 69 TRP cc_start: 0.7950 (m-90) cc_final: 0.7253 (m-90) REVERT: E 104 MET cc_start: 0.8105 (mmm) cc_final: 0.7894 (tpp) REVERT: E 111 LEU cc_start: 0.9031 (mt) cc_final: 0.8797 (tp) REVERT: E 293 GLU cc_start: 0.8128 (tt0) cc_final: 0.7851 (tm-30) REVERT: E 373 MET cc_start: 0.9044 (mmp) cc_final: 0.8598 (mmt) REVERT: E 426 MET cc_start: 0.6995 (mmm) cc_final: 0.6747 (mmm) REVERT: E 427 TRP cc_start: 0.7660 (m-90) cc_final: 0.7252 (m-90) REVERT: F 539 VAL cc_start: 0.9689 (t) cc_final: 0.9452 (p) REVERT: F 629 MET cc_start: 0.8215 (mtp) cc_final: 0.7812 (mtm) REVERT: F 630 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8091 (mt-10) REVERT: F 640 SER cc_start: 0.9276 (m) cc_final: 0.9009 (p) REVERT: G 35 TYR cc_start: 0.8853 (m-80) cc_final: 0.8563 (m-10) REVERT: G 76 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9187 (mmmm) REVERT: I 27 GLU cc_start: 0.8645 (tp30) cc_final: 0.8431 (tp30) REVERT: I 89 MET cc_start: 0.8562 (ttt) cc_final: 0.7685 (ttt) REVERT: H 1 ARG cc_start: 0.7130 (ttp80) cc_final: 0.5677 (ttm-80) REVERT: H 45 LEU cc_start: 0.8797 (tp) cc_final: 0.8572 (tp) REVERT: H 90 ASP cc_start: 0.9140 (m-30) cc_final: 0.8881 (m-30) REVERT: L 17 GLN cc_start: 0.8420 (tt0) cc_final: 0.8166 (tm-30) REVERT: L 21 ILE cc_start: 0.7749 (mt) cc_final: 0.7305 (pt) REVERT: L 92 LYS cc_start: 0.9203 (tptp) cc_final: 0.8455 (tppp) REVERT: L 103 LYS cc_start: 0.8453 (tttt) cc_final: 0.8183 (tmtt) outliers start: 9 outliers final: 1 residues processed: 384 average time/residue: 0.3581 time to fit residues: 198.9531 Evaluate side-chains 194 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 216 HIS A 300 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN C 66 HIS C 82 GLN C 287 GLN C 300 ASN D 590 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN E 105 HIS E 302 ASN E 339 ASN E 344 GLN E 422 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 115 ASN L 45 GLN L 53 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19228 Z= 0.269 Angle : 0.760 11.941 26090 Z= 0.374 Chirality : 0.052 0.434 3308 Planarity : 0.005 0.050 3132 Dihedral : 14.492 102.598 4898 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 2131 helix: -2.34 (0.22), residues: 345 sheet: -2.43 (0.20), residues: 533 loop : -2.74 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 479 HIS 0.006 0.001 HIS C 374 PHE 0.024 0.002 PHE A 277 TYR 0.021 0.002 TYR A 217 ARG 0.006 0.001 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8090 (m90) cc_final: 0.7656 (m90) REVERT: A 69 TRP cc_start: 0.8262 (m-90) cc_final: 0.7922 (m-90) REVERT: A 106 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7853 (pt0) REVERT: A 107 ASP cc_start: 0.8783 (m-30) cc_final: 0.8523 (m-30) REVERT: A 211 GLU cc_start: 0.8359 (mp0) cc_final: 0.8081 (mp0) REVERT: A 434 MET cc_start: 0.8777 (tmm) cc_final: 0.8439 (tmm) REVERT: B 638 TYR cc_start: 0.9097 (m-80) cc_final: 0.8750 (m-10) REVERT: B 657 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8928 (mp0) REVERT: B 659 GLU cc_start: 0.9484 (tt0) cc_final: 0.9113 (tm-30) REVERT: C 42 VAL cc_start: 0.9427 (t) cc_final: 0.9216 (p) REVERT: C 304 ARG cc_start: 0.8132 (tpm170) cc_final: 0.7871 (mmm160) REVERT: D 620 ASN cc_start: 0.9134 (m-40) cc_final: 0.8694 (t0) REVERT: D 632 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8187 (tm-30) REVERT: D 650 GLN cc_start: 0.8700 (tt0) cc_final: 0.8481 (tt0) REVERT: D 657 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8387 (tm-30) REVERT: E 69 TRP cc_start: 0.7948 (m-90) cc_final: 0.7293 (m-90) REVERT: E 373 MET cc_start: 0.9057 (mmp) cc_final: 0.8565 (mmt) REVERT: E 427 TRP cc_start: 0.7964 (m-90) cc_final: 0.7339 (m-90) REVERT: E 475 MET cc_start: 0.7958 (mmm) cc_final: 0.7750 (mmm) REVERT: F 586 TYR cc_start: 0.9014 (t80) cc_final: 0.8368 (t80) REVERT: F 601 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8650 (mtmm) REVERT: F 640 SER cc_start: 0.9321 (m) cc_final: 0.9049 (p) REVERT: I 4 MET cc_start: 0.6918 (tmm) cc_final: 0.6713 (ppp) REVERT: H 45 LEU cc_start: 0.8851 (tp) cc_final: 0.8651 (tp) REVERT: H 90 ASP cc_start: 0.9063 (m-30) cc_final: 0.8850 (m-30) REVERT: H 108 LEU cc_start: 0.9279 (tp) cc_final: 0.9024 (tt) REVERT: L 17 GLN cc_start: 0.8563 (tt0) cc_final: 0.8114 (tm-30) REVERT: L 27 GLU cc_start: 0.7865 (tp30) cc_final: 0.7657 (tm-30) REVERT: L 73 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7641 (tp) REVERT: L 74 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7735 (mmm160) REVERT: L 75 ILE cc_start: 0.7710 (mm) cc_final: 0.7236 (tt) REVERT: L 92 LYS cc_start: 0.9194 (tptp) cc_final: 0.8773 (tppp) REVERT: L 103 LYS cc_start: 0.8483 (tttt) cc_final: 0.8185 (tmtt) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3167 time to fit residues: 132.2608 Evaluate side-chains 197 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN C 339 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19228 Z= 0.187 Angle : 0.677 10.421 26090 Z= 0.329 Chirality : 0.050 0.396 3308 Planarity : 0.004 0.049 3132 Dihedral : 12.890 95.881 4898 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.17), residues: 2131 helix: -1.75 (0.25), residues: 349 sheet: -2.07 (0.20), residues: 556 loop : -2.56 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 338 HIS 0.004 0.001 HIS E 374 PHE 0.012 0.001 PHE I 49 TYR 0.026 0.001 TYR A 217 ARG 0.005 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8102 (m90) cc_final: 0.7524 (m90) REVERT: A 69 TRP cc_start: 0.8285 (m-90) cc_final: 0.7810 (m-90) REVERT: A 106 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7847 (pt0) REVERT: A 211 GLU cc_start: 0.8305 (mp0) cc_final: 0.8022 (mp0) REVERT: A 284 ILE cc_start: 0.9619 (mt) cc_final: 0.9403 (tt) REVERT: A 434 MET cc_start: 0.8802 (tmm) cc_final: 0.8471 (tmm) REVERT: B 638 TYR cc_start: 0.9089 (m-80) cc_final: 0.8803 (m-10) REVERT: B 645 LEU cc_start: 0.9508 (tt) cc_final: 0.9244 (tt) REVERT: B 659 GLU cc_start: 0.9464 (tt0) cc_final: 0.9108 (tm-30) REVERT: C 42 VAL cc_start: 0.9358 (t) cc_final: 0.9130 (p) REVERT: C 46 LYS cc_start: 0.9129 (mttt) cc_final: 0.8916 (mttm) REVERT: C 304 ARG cc_start: 0.8148 (tpm170) cc_final: 0.7753 (mmm160) REVERT: C 427 TRP cc_start: 0.3697 (t60) cc_final: 0.3124 (t60) REVERT: D 530 MET cc_start: 0.7919 (ptm) cc_final: 0.7716 (ptp) REVERT: D 589 ASP cc_start: 0.9322 (m-30) cc_final: 0.9122 (m-30) REVERT: D 591 GLN cc_start: 0.8840 (tt0) cc_final: 0.8248 (tt0) REVERT: D 620 ASN cc_start: 0.9093 (m-40) cc_final: 0.8735 (t0) REVERT: D 629 MET cc_start: 0.8707 (tpp) cc_final: 0.8352 (tpp) REVERT: D 632 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8163 (tm-30) REVERT: D 648 ASP cc_start: 0.8704 (t70) cc_final: 0.8492 (t0) REVERT: D 654 GLU cc_start: 0.9056 (tp30) cc_final: 0.8516 (tp30) REVERT: D 661 LEU cc_start: 0.9230 (tp) cc_final: 0.8963 (pp) REVERT: E 42 VAL cc_start: 0.9116 (t) cc_final: 0.8769 (p) REVERT: E 69 TRP cc_start: 0.7859 (m-90) cc_final: 0.7321 (m-90) REVERT: E 95 MET cc_start: 0.9282 (ptm) cc_final: 0.9000 (ptm) REVERT: E 104 MET cc_start: 0.9210 (mtt) cc_final: 0.8987 (ttm) REVERT: E 373 MET cc_start: 0.9066 (mmp) cc_final: 0.8590 (mmt) REVERT: E 434 MET cc_start: 0.7914 (ttp) cc_final: 0.7583 (ptp) REVERT: F 586 TYR cc_start: 0.9003 (t80) cc_final: 0.8546 (t80) REVERT: F 601 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8712 (mtmm) REVERT: F 626 MET cc_start: 0.6766 (tmm) cc_final: 0.6380 (tmm) REVERT: F 640 SER cc_start: 0.9339 (m) cc_final: 0.9064 (p) REVERT: G 35 TYR cc_start: 0.8513 (m-10) cc_final: 0.7859 (m-10) REVERT: I 89 MET cc_start: 0.8430 (ttt) cc_final: 0.6996 (ttt) REVERT: H 45 LEU cc_start: 0.8825 (tp) cc_final: 0.8530 (tp) REVERT: H 90 ASP cc_start: 0.9055 (m-30) cc_final: 0.8778 (m-30) REVERT: H 99 MET cc_start: 0.7442 (ttt) cc_final: 0.7201 (mtp) REVERT: H 101 GLN cc_start: 0.8116 (mt0) cc_final: 0.7733 (mt0) REVERT: H 108 LEU cc_start: 0.9368 (tp) cc_final: 0.9144 (tt) REVERT: L 17 GLN cc_start: 0.8491 (tt0) cc_final: 0.8147 (tm-30) REVERT: L 74 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7644 (mmm160) REVERT: L 92 LYS cc_start: 0.9247 (tptp) cc_final: 0.8778 (tppp) REVERT: L 103 LYS cc_start: 0.8426 (tttt) cc_final: 0.8042 (tmtt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3244 time to fit residues: 131.5871 Evaluate side-chains 189 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19228 Z= 0.278 Angle : 0.713 10.814 26090 Z= 0.345 Chirality : 0.050 0.395 3308 Planarity : 0.004 0.048 3132 Dihedral : 12.091 92.853 4898 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.17), residues: 2131 helix: -1.52 (0.26), residues: 355 sheet: -1.95 (0.20), residues: 549 loop : -2.55 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 125 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.002 PHE A 277 TYR 0.024 0.002 TYR A 217 ARG 0.004 0.000 ARG F 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8119 (m90) cc_final: 0.7683 (m90) REVERT: A 69 TRP cc_start: 0.8327 (m-90) cc_final: 0.7752 (m-90) REVERT: A 106 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7890 (pt0) REVERT: A 107 ASP cc_start: 0.8833 (m-30) cc_final: 0.8555 (m-30) REVERT: A 211 GLU cc_start: 0.8360 (mp0) cc_final: 0.8077 (mp0) REVERT: A 434 MET cc_start: 0.8793 (tmm) cc_final: 0.8446 (tmm) REVERT: B 638 TYR cc_start: 0.9140 (m-80) cc_final: 0.8857 (m-10) REVERT: B 647 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 659 GLU cc_start: 0.9483 (tt0) cc_final: 0.9152 (tm-30) REVERT: C 42 VAL cc_start: 0.9328 (t) cc_final: 0.9116 (p) REVERT: C 304 ARG cc_start: 0.8406 (tpm170) cc_final: 0.7764 (mmm160) REVERT: D 601 LYS cc_start: 0.8200 (mttp) cc_final: 0.7920 (mttp) REVERT: D 620 ASN cc_start: 0.9113 (m-40) cc_final: 0.8765 (t0) REVERT: D 629 MET cc_start: 0.8624 (tpp) cc_final: 0.8376 (tpp) REVERT: D 632 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8134 (tm-30) REVERT: D 661 LEU cc_start: 0.9323 (tp) cc_final: 0.9038 (pp) REVERT: E 42 VAL cc_start: 0.9244 (t) cc_final: 0.8852 (p) REVERT: E 69 TRP cc_start: 0.7666 (m-90) cc_final: 0.7010 (m-90) REVERT: E 104 MET cc_start: 0.9342 (mtt) cc_final: 0.9101 (ttm) REVERT: E 373 MET cc_start: 0.9073 (mmp) cc_final: 0.8569 (mmt) REVERT: F 519 PHE cc_start: 0.8835 (m-80) cc_final: 0.8631 (m-80) REVERT: F 586 TYR cc_start: 0.9128 (t80) cc_final: 0.8573 (t80) REVERT: F 630 GLU cc_start: 0.9173 (pt0) cc_final: 0.8908 (pt0) REVERT: F 640 SER cc_start: 0.9352 (m) cc_final: 0.9125 (p) REVERT: F 647 GLU cc_start: 0.9184 (tt0) cc_final: 0.8968 (tm-30) REVERT: G 34 MET cc_start: 0.9124 (tpp) cc_final: 0.8897 (mmm) REVERT: G 99 MET cc_start: 0.8634 (tpp) cc_final: 0.7902 (tpt) REVERT: I 4 MET cc_start: 0.7215 (tmm) cc_final: 0.6935 (tmm) REVERT: H 90 ASP cc_start: 0.9056 (m-30) cc_final: 0.8754 (m-30) REVERT: H 108 LEU cc_start: 0.9439 (tp) cc_final: 0.9227 (tt) REVERT: L 27 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7261 (tm-30) REVERT: L 92 LYS cc_start: 0.9260 (tptp) cc_final: 0.8827 (tppp) REVERT: L 103 LYS cc_start: 0.8426 (tttt) cc_final: 0.8061 (tmtt) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3033 time to fit residues: 111.8532 Evaluate side-chains 181 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 overall best weight: 2.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19228 Z= 0.243 Angle : 0.689 11.209 26090 Z= 0.333 Chirality : 0.050 0.398 3308 Planarity : 0.004 0.047 3132 Dihedral : 11.490 93.125 4898 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.10 % Allowed : 1.82 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.17), residues: 2131 helix: -1.19 (0.27), residues: 348 sheet: -1.87 (0.21), residues: 547 loop : -2.50 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 427 HIS 0.004 0.001 HIS C 374 PHE 0.012 0.001 PHE I 49 TYR 0.019 0.001 TYR I 34 ARG 0.007 0.000 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7991 (m90) cc_final: 0.7543 (m90) REVERT: A 69 TRP cc_start: 0.8326 (m-90) cc_final: 0.7780 (m-90) REVERT: A 106 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7942 (pt0) REVERT: A 211 GLU cc_start: 0.8352 (mp0) cc_final: 0.8096 (mp0) REVERT: A 434 MET cc_start: 0.8784 (tmm) cc_final: 0.8399 (tmm) REVERT: B 585 ARG cc_start: 0.9289 (mtp-110) cc_final: 0.9020 (mmm-85) REVERT: B 638 TYR cc_start: 0.9127 (m-80) cc_final: 0.8815 (m-10) REVERT: B 659 GLU cc_start: 0.9485 (tt0) cc_final: 0.9157 (tm-30) REVERT: C 42 VAL cc_start: 0.9331 (t) cc_final: 0.9122 (p) REVERT: C 304 ARG cc_start: 0.8192 (tpm170) cc_final: 0.7722 (mmm160) REVERT: D 530 MET cc_start: 0.8128 (ptm) cc_final: 0.7737 (ptm) REVERT: D 591 GLN cc_start: 0.8919 (tt0) cc_final: 0.8303 (tt0) REVERT: D 601 LYS cc_start: 0.8015 (mttp) cc_final: 0.7760 (mttp) REVERT: D 620 ASN cc_start: 0.9078 (m-40) cc_final: 0.8763 (t0) REVERT: D 632 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8157 (tm-30) REVERT: D 648 ASP cc_start: 0.8841 (t70) cc_final: 0.8628 (t0) REVERT: D 655 LYS cc_start: 0.9434 (mmtm) cc_final: 0.9189 (mmmm) REVERT: D 661 LEU cc_start: 0.9309 (tp) cc_final: 0.9040 (pp) REVERT: E 69 TRP cc_start: 0.7611 (m-90) cc_final: 0.6920 (m-90) REVERT: E 210 PHE cc_start: 0.8729 (m-80) cc_final: 0.8460 (m-10) REVERT: E 373 MET cc_start: 0.9061 (mmp) cc_final: 0.8637 (mmt) REVERT: F 586 TYR cc_start: 0.9128 (t80) cc_final: 0.8622 (t80) REVERT: F 640 SER cc_start: 0.9381 (m) cc_final: 0.9159 (p) REVERT: G 35 TYR cc_start: 0.8220 (m-10) cc_final: 0.7647 (m-10) REVERT: G 99 MET cc_start: 0.8613 (tpp) cc_final: 0.7374 (tpt) REVERT: H 90 ASP cc_start: 0.9058 (m-30) cc_final: 0.8753 (m-30) REVERT: H 99 MET cc_start: 0.7775 (ttm) cc_final: 0.7217 (mtp) REVERT: L 18 PRO cc_start: 0.8732 (Cg_endo) cc_final: 0.8228 (Cg_exo) REVERT: L 27 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7480 (tm-30) REVERT: L 92 LYS cc_start: 0.9271 (tptp) cc_final: 0.8787 (tppp) REVERT: L 103 LYS cc_start: 0.8361 (tttt) cc_final: 0.7992 (tmtt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3062 time to fit residues: 112.8790 Evaluate side-chains 183 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19228 Z= 0.321 Angle : 0.743 11.415 26090 Z= 0.357 Chirality : 0.051 0.386 3308 Planarity : 0.004 0.047 3132 Dihedral : 11.264 92.032 4898 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.17), residues: 2131 helix: -1.21 (0.27), residues: 359 sheet: -1.88 (0.21), residues: 546 loop : -2.50 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 427 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.002 PHE A 277 TYR 0.021 0.002 TYR A 217 ARG 0.005 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8081 (m90) cc_final: 0.7532 (m90) REVERT: A 69 TRP cc_start: 0.8369 (m-90) cc_final: 0.7849 (m-90) REVERT: A 106 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7935 (pt0) REVERT: A 107 ASP cc_start: 0.8930 (m-30) cc_final: 0.8611 (m-30) REVERT: A 211 GLU cc_start: 0.8400 (mp0) cc_final: 0.8160 (mp0) REVERT: A 426 MET cc_start: 0.7800 (ttp) cc_final: 0.7572 (ttp) REVERT: A 434 MET cc_start: 0.8695 (tmm) cc_final: 0.7940 (tmm) REVERT: B 638 TYR cc_start: 0.9172 (m-80) cc_final: 0.8798 (m-10) REVERT: B 659 GLU cc_start: 0.9519 (tt0) cc_final: 0.9176 (tm-30) REVERT: D 530 MET cc_start: 0.8138 (ptm) cc_final: 0.7812 (ptm) REVERT: D 601 LYS cc_start: 0.8084 (mttp) cc_final: 0.7793 (mttp) REVERT: D 620 ASN cc_start: 0.9130 (m-40) cc_final: 0.8800 (t0) REVERT: D 629 MET cc_start: 0.8980 (tpp) cc_final: 0.8214 (tpp) REVERT: D 632 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8192 (tm-30) REVERT: D 655 LYS cc_start: 0.9451 (mmtm) cc_final: 0.9117 (mmmm) REVERT: D 658 GLN cc_start: 0.9331 (pp30) cc_final: 0.9123 (pp30) REVERT: D 661 LEU cc_start: 0.9346 (tp) cc_final: 0.9078 (pp) REVERT: E 42 VAL cc_start: 0.9228 (t) cc_final: 0.8883 (p) REVERT: E 69 TRP cc_start: 0.7726 (m-90) cc_final: 0.6984 (m-90) REVERT: E 373 MET cc_start: 0.9053 (mmp) cc_final: 0.8595 (mmt) REVERT: F 586 TYR cc_start: 0.9196 (t80) cc_final: 0.8601 (t80) REVERT: F 622 ILE cc_start: 0.7296 (mm) cc_final: 0.6971 (mm) REVERT: F 630 GLU cc_start: 0.9209 (pt0) cc_final: 0.8986 (pt0) REVERT: F 640 SER cc_start: 0.9427 (m) cc_final: 0.9201 (p) REVERT: G 35 TYR cc_start: 0.8334 (m-10) cc_final: 0.7746 (m-10) REVERT: G 99 MET cc_start: 0.8565 (tpp) cc_final: 0.7264 (tpt) REVERT: I 4 MET cc_start: 0.7344 (tmm) cc_final: 0.7123 (tmm) REVERT: H 90 ASP cc_start: 0.9056 (m-30) cc_final: 0.8747 (m-30) REVERT: H 99 MET cc_start: 0.7912 (ttm) cc_final: 0.7311 (mtp) REVERT: L 27 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7523 (tm-30) REVERT: L 92 LYS cc_start: 0.9223 (tptp) cc_final: 0.8734 (tppp) REVERT: L 103 LYS cc_start: 0.8313 (tttt) cc_final: 0.7931 (tmtt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3351 time to fit residues: 118.3183 Evaluate side-chains 177 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 150 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 115 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 287 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19228 Z= 0.156 Angle : 0.651 10.893 26090 Z= 0.313 Chirality : 0.049 0.350 3308 Planarity : 0.004 0.046 3132 Dihedral : 10.247 93.931 4898 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.82 (0.17), residues: 2131 helix: -0.94 (0.27), residues: 358 sheet: -1.61 (0.21), residues: 553 loop : -2.35 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 427 HIS 0.005 0.001 HIS C 374 PHE 0.014 0.001 PHE I 49 TYR 0.022 0.001 TYR I 34 ARG 0.006 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8340 (m-90) cc_final: 0.7843 (m-90) REVERT: A 106 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7927 (pt0) REVERT: A 107 ASP cc_start: 0.8896 (m-30) cc_final: 0.8665 (m-30) REVERT: A 176 PHE cc_start: 0.8710 (m-10) cc_final: 0.8402 (m-10) REVERT: A 211 GLU cc_start: 0.8268 (mp0) cc_final: 0.8036 (mp0) REVERT: A 434 MET cc_start: 0.8691 (tmm) cc_final: 0.8416 (tmm) REVERT: B 638 TYR cc_start: 0.9103 (m-80) cc_final: 0.8836 (m-10) REVERT: B 643 TYR cc_start: 0.9193 (m-10) cc_final: 0.8755 (m-80) REVERT: B 659 GLU cc_start: 0.9491 (tt0) cc_final: 0.9188 (tm-30) REVERT: C 95 MET cc_start: 0.9135 (ptm) cc_final: 0.8913 (ppp) REVERT: C 492 GLU cc_start: 0.8696 (pm20) cc_final: 0.8486 (pm20) REVERT: D 530 MET cc_start: 0.8130 (ptm) cc_final: 0.7816 (ptm) REVERT: D 620 ASN cc_start: 0.9105 (m-40) cc_final: 0.8752 (t0) REVERT: D 629 MET cc_start: 0.8901 (tpp) cc_final: 0.8465 (tpp) REVERT: D 632 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8231 (tm-30) REVERT: D 655 LYS cc_start: 0.9438 (mmtm) cc_final: 0.9047 (mmmm) REVERT: D 661 LEU cc_start: 0.9293 (tp) cc_final: 0.9033 (pp) REVERT: E 42 VAL cc_start: 0.9114 (t) cc_final: 0.8781 (p) REVERT: E 69 TRP cc_start: 0.7609 (m-90) cc_final: 0.6918 (m-90) REVERT: E 95 MET cc_start: 0.9207 (ptm) cc_final: 0.8946 (ptm) REVERT: E 104 MET cc_start: 0.8892 (ttm) cc_final: 0.8569 (ttm) REVERT: E 210 PHE cc_start: 0.8681 (m-80) cc_final: 0.8389 (m-10) REVERT: E 277 PHE cc_start: 0.7694 (p90) cc_final: 0.7476 (p90) REVERT: E 373 MET cc_start: 0.9001 (mmp) cc_final: 0.8598 (mmt) REVERT: F 586 TYR cc_start: 0.9083 (t80) cc_final: 0.8638 (t80) REVERT: F 640 SER cc_start: 0.9365 (m) cc_final: 0.9117 (p) REVERT: G 35 TYR cc_start: 0.8163 (m-10) cc_final: 0.7813 (m-10) REVERT: G 99 MET cc_start: 0.8627 (tpp) cc_final: 0.7303 (tpt) REVERT: I 4 MET cc_start: 0.7238 (tmm) cc_final: 0.6982 (tmm) REVERT: I 98 PHE cc_start: 0.8462 (m-80) cc_final: 0.7862 (m-10) REVERT: H 29 PHE cc_start: 0.8647 (t80) cc_final: 0.8410 (t80) REVERT: H 90 ASP cc_start: 0.9033 (m-30) cc_final: 0.8556 (m-30) REVERT: L 27 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7471 (tm-30) REVERT: L 92 LYS cc_start: 0.9177 (tptp) cc_final: 0.8721 (tppp) REVERT: L 103 LYS cc_start: 0.8252 (tttt) cc_final: 0.7777 (tmtt) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3070 time to fit residues: 122.7629 Evaluate side-chains 186 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 101 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 161 optimal weight: 0.0030 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 287 GLN A 478 ASN B 564 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19228 Z= 0.155 Angle : 0.652 9.555 26090 Z= 0.312 Chirality : 0.049 0.532 3308 Planarity : 0.004 0.049 3132 Dihedral : 9.716 90.140 4898 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.71 (0.17), residues: 2131 helix: -0.91 (0.27), residues: 357 sheet: -1.49 (0.20), residues: 582 loop : -2.28 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 427 HIS 0.004 0.001 HIS C 374 PHE 0.016 0.001 PHE E 176 TYR 0.023 0.001 TYR I 34 ARG 0.004 0.000 ARG B 633 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8350 (m-90) cc_final: 0.7848 (m-90) REVERT: A 106 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7922 (pt0) REVERT: A 107 ASP cc_start: 0.8877 (m-30) cc_final: 0.8645 (m-30) REVERT: A 165 MET cc_start: 0.8304 (mtm) cc_final: 0.8026 (mtp) REVERT: A 176 PHE cc_start: 0.8763 (m-10) cc_final: 0.8479 (m-10) REVERT: A 211 GLU cc_start: 0.8194 (mp0) cc_final: 0.7943 (mp0) REVERT: A 426 MET cc_start: 0.7661 (ttp) cc_final: 0.7232 (ttp) REVERT: A 434 MET cc_start: 0.8681 (tmm) cc_final: 0.7836 (tmm) REVERT: B 638 TYR cc_start: 0.9114 (m-80) cc_final: 0.8828 (m-10) REVERT: B 647 GLU cc_start: 0.8675 (mp0) cc_final: 0.8443 (mp0) REVERT: B 659 GLU cc_start: 0.9522 (tt0) cc_final: 0.9173 (tm-30) REVERT: C 427 TRP cc_start: 0.5005 (t60) cc_final: 0.4552 (t60) REVERT: D 530 MET cc_start: 0.8077 (ptm) cc_final: 0.7811 (ptm) REVERT: D 591 GLN cc_start: 0.8879 (tt0) cc_final: 0.8322 (tt0) REVERT: D 620 ASN cc_start: 0.9114 (m-40) cc_final: 0.8809 (t0) REVERT: D 629 MET cc_start: 0.8913 (tpp) cc_final: 0.8521 (tpp) REVERT: D 632 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8187 (tm-30) REVERT: D 655 LYS cc_start: 0.9430 (mmtm) cc_final: 0.9120 (mmmm) REVERT: D 661 LEU cc_start: 0.9304 (tp) cc_final: 0.9051 (pp) REVERT: E 42 VAL cc_start: 0.9128 (t) cc_final: 0.8805 (p) REVERT: E 69 TRP cc_start: 0.7420 (m-90) cc_final: 0.6836 (m-90) REVERT: E 95 MET cc_start: 0.9205 (ptm) cc_final: 0.8966 (ptm) REVERT: E 104 MET cc_start: 0.8898 (ttm) cc_final: 0.8529 (ttm) REVERT: E 210 PHE cc_start: 0.8690 (m-80) cc_final: 0.8408 (m-10) REVERT: E 373 MET cc_start: 0.8919 (mmp) cc_final: 0.8465 (mmt) REVERT: F 586 TYR cc_start: 0.9097 (t80) cc_final: 0.8712 (t80) REVERT: F 640 SER cc_start: 0.9403 (m) cc_final: 0.9165 (p) REVERT: G 99 MET cc_start: 0.8669 (tpp) cc_final: 0.7012 (tpt) REVERT: I 4 MET cc_start: 0.7244 (tmm) cc_final: 0.7009 (tmm) REVERT: I 98 PHE cc_start: 0.8431 (m-80) cc_final: 0.7401 (m-80) REVERT: H 29 PHE cc_start: 0.8586 (t80) cc_final: 0.8372 (t80) REVERT: H 90 ASP cc_start: 0.9027 (m-30) cc_final: 0.8547 (m-30) REVERT: H 99 MET cc_start: 0.7321 (ttt) cc_final: 0.6845 (mtp) REVERT: L 27 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7547 (tm-30) REVERT: L 92 LYS cc_start: 0.9230 (tptp) cc_final: 0.8249 (tppp) REVERT: L 103 LYS cc_start: 0.8234 (tttt) cc_final: 0.7743 (tmtt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3018 time to fit residues: 118.9588 Evaluate side-chains 191 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 10.0000 chunk 196 optimal weight: 0.0050 chunk 179 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 180 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19228 Z= 0.362 Angle : 0.776 11.610 26090 Z= 0.373 Chirality : 0.051 0.442 3308 Planarity : 0.004 0.046 3132 Dihedral : 10.281 86.346 4898 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.85 (0.17), residues: 2131 helix: -0.92 (0.27), residues: 357 sheet: -1.69 (0.20), residues: 573 loop : -2.34 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 427 HIS 0.008 0.002 HIS C 105 PHE 0.016 0.002 PHE A 277 TYR 0.025 0.002 TYR B 643 ARG 0.006 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8374 (m-90) cc_final: 0.7942 (m-90) REVERT: A 106 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7983 (pt0) REVERT: A 107 ASP cc_start: 0.8959 (m-30) cc_final: 0.8717 (m-30) REVERT: A 211 GLU cc_start: 0.8326 (mp0) cc_final: 0.8068 (mp0) REVERT: A 426 MET cc_start: 0.7745 (ttp) cc_final: 0.7532 (ttp) REVERT: A 434 MET cc_start: 0.8648 (tmm) cc_final: 0.7788 (tmm) REVERT: B 659 GLU cc_start: 0.9561 (tt0) cc_final: 0.9191 (tm-30) REVERT: D 530 MET cc_start: 0.8136 (ptm) cc_final: 0.7889 (ptm) REVERT: D 591 GLN cc_start: 0.8985 (tt0) cc_final: 0.8187 (tt0) REVERT: D 620 ASN cc_start: 0.9182 (m-40) cc_final: 0.8832 (t0) REVERT: D 629 MET cc_start: 0.8997 (tpp) cc_final: 0.8407 (tpp) REVERT: D 632 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8204 (tm-30) REVERT: D 636 ASP cc_start: 0.9370 (t70) cc_final: 0.9157 (t0) REVERT: D 647 GLU cc_start: 0.9713 (pm20) cc_final: 0.9474 (pm20) REVERT: E 69 TRP cc_start: 0.7697 (m-90) cc_final: 0.7030 (m-90) REVERT: E 104 MET cc_start: 0.8997 (ttm) cc_final: 0.8521 (ttm) REVERT: E 373 MET cc_start: 0.8881 (mmp) cc_final: 0.8405 (mmt) REVERT: F 586 TYR cc_start: 0.9243 (t80) cc_final: 0.8577 (t80) REVERT: F 640 SER cc_start: 0.9466 (m) cc_final: 0.9203 (p) REVERT: F 649 SER cc_start: 0.8887 (m) cc_final: 0.8676 (p) REVERT: G 35 TYR cc_start: 0.8356 (m-80) cc_final: 0.7565 (m-10) REVERT: G 99 MET cc_start: 0.8335 (tpp) cc_final: 0.7602 (tpt) REVERT: I 4 MET cc_start: 0.7229 (tmm) cc_final: 0.7020 (tmm) REVERT: I 36 TYR cc_start: 0.7829 (p90) cc_final: 0.7189 (p90) REVERT: I 89 MET cc_start: 0.8360 (ttp) cc_final: 0.6438 (ttp) REVERT: I 98 PHE cc_start: 0.8522 (m-80) cc_final: 0.7033 (m-80) REVERT: H 90 ASP cc_start: 0.9043 (m-30) cc_final: 0.8712 (m-30) REVERT: H 99 MET cc_start: 0.7578 (ttt) cc_final: 0.6646 (mtp) REVERT: L 27 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7439 (tm-30) REVERT: L 92 LYS cc_start: 0.8982 (tptp) cc_final: 0.8629 (tppp) REVERT: L 103 LYS cc_start: 0.8351 (tttt) cc_final: 0.7914 (tmtt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2940 time to fit residues: 104.5215 Evaluate side-chains 174 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 0.0030 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 656 ASN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19228 Z= 0.219 Angle : 0.674 11.681 26090 Z= 0.324 Chirality : 0.049 0.424 3308 Planarity : 0.004 0.048 3132 Dihedral : 9.869 87.797 4898 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.16 % Allowed : 0.05 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.62 (0.17), residues: 2131 helix: -0.72 (0.27), residues: 362 sheet: -1.46 (0.21), residues: 533 loop : -2.25 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 45 HIS 0.007 0.001 HIS C 105 PHE 0.012 0.001 PHE E 176 TYR 0.026 0.001 TYR B 638 ARG 0.005 0.000 ARG B 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8337 (m-90) cc_final: 0.7881 (m-90) REVERT: A 106 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7962 (pt0) REVERT: A 107 ASP cc_start: 0.8929 (m-30) cc_final: 0.8710 (m-30) REVERT: A 176 PHE cc_start: 0.8685 (m-10) cc_final: 0.8359 (m-10) REVERT: A 211 GLU cc_start: 0.8252 (mp0) cc_final: 0.8005 (mp0) REVERT: A 426 MET cc_start: 0.7685 (ttp) cc_final: 0.7199 (ttp) REVERT: A 434 MET cc_start: 0.8646 (tmm) cc_final: 0.7766 (tmm) REVERT: B 659 GLU cc_start: 0.9520 (tt0) cc_final: 0.9167 (tm-30) REVERT: C 104 MET cc_start: 0.8380 (tpp) cc_final: 0.8114 (tpp) REVERT: D 530 MET cc_start: 0.8133 (ptm) cc_final: 0.7872 (ptm) REVERT: D 538 THR cc_start: 0.9674 (p) cc_final: 0.9466 (p) REVERT: D 591 GLN cc_start: 0.8948 (tt0) cc_final: 0.8285 (tt0) REVERT: D 620 ASN cc_start: 0.9175 (m-40) cc_final: 0.8791 (t0) REVERT: D 629 MET cc_start: 0.8930 (tpp) cc_final: 0.8439 (tpp) REVERT: D 632 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8250 (tm-30) REVERT: D 647 GLU cc_start: 0.9685 (pm20) cc_final: 0.9392 (pm20) REVERT: D 655 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9155 (mmtp) REVERT: E 42 VAL cc_start: 0.9162 (t) cc_final: 0.8836 (p) REVERT: E 69 TRP cc_start: 0.7680 (m-90) cc_final: 0.6996 (m-90) REVERT: E 104 MET cc_start: 0.8782 (ttm) cc_final: 0.8485 (ttm) REVERT: E 210 PHE cc_start: 0.8701 (m-80) cc_final: 0.8329 (m-10) REVERT: E 373 MET cc_start: 0.8865 (mmp) cc_final: 0.8392 (mmt) REVERT: F 586 TYR cc_start: 0.9161 (t80) cc_final: 0.8620 (t80) REVERT: G 35 TYR cc_start: 0.8292 (m-80) cc_final: 0.7675 (m-10) REVERT: G 99 MET cc_start: 0.8300 (tpp) cc_final: 0.7457 (tpt) REVERT: I 4 MET cc_start: 0.7217 (tmm) cc_final: 0.6914 (tmm) REVERT: I 36 TYR cc_start: 0.7735 (p90) cc_final: 0.6772 (p90) REVERT: I 89 MET cc_start: 0.8238 (ttp) cc_final: 0.6537 (ttp) REVERT: I 98 PHE cc_start: 0.8492 (m-80) cc_final: 0.7033 (m-80) REVERT: H 90 ASP cc_start: 0.9034 (m-30) cc_final: 0.8676 (m-30) REVERT: H 99 MET cc_start: 0.7357 (ttt) cc_final: 0.6658 (mtp) REVERT: L 27 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7499 (tm-30) REVERT: L 92 LYS cc_start: 0.8867 (tptp) cc_final: 0.8595 (tppp) REVERT: L 103 LYS cc_start: 0.8361 (tttt) cc_final: 0.7898 (tmtt) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.3028 time to fit residues: 110.1824 Evaluate side-chains 179 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048516 restraints weight = 98264.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049870 restraints weight = 57225.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050764 restraints weight = 39995.479| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19228 Z= 0.234 Angle : 0.682 11.187 26090 Z= 0.327 Chirality : 0.049 0.388 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.741 86.218 4898 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.61 (0.17), residues: 2131 helix: -0.65 (0.27), residues: 361 sheet: -1.49 (0.21), residues: 551 loop : -2.24 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 111 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.001 PHE E 176 TYR 0.024 0.001 TYR B 643 ARG 0.005 0.000 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.31 seconds wall clock time: 67 minutes 43.94 seconds (4063.94 seconds total)