Starting phenix.real_space_refine on Fri Sep 27 08:05:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7t_23218/09_2024/7l7t_23218.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 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 105 5.16 5 C 9603 2.51 5 N 2565 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15423 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "C" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "E" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "F" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "G" 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: "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: 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: "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: "L" 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: 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: "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: 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: "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: 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: "W" 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: "X" 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: "Y" 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: "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: 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: "c" 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: "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: 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: "f" 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 8.67, per 1000 atoms: 0.56 Number of scatterers: 15423 At special positions: 0 Unit cell: (129.95, 125.35, 123.05, 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 105 16.00 O 3150 8.00 N 2565 7.00 C 9603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 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 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 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 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 601 " - " ASN A 276 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 363 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 133 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 355 " " NAG A 610 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 276 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 289 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 355 " " NAG E 610 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 241 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 448 " " NAG R 1 " - " ASN C 295 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 301 " " NAG V 1 " - " ASN C 241 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN E 448 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 241 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 160 " Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 1.9 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 30 sheets defined 31.9% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.926A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 542 through 557 Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.513A pdb=" N LEU B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.927A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 542 through 557 Processing helix chain 'D' and resid 558 through 568 removed outlier: 3.514A pdb=" N LEU D 566 " --> pdb=" O GLN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.927A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 542 through 557 Processing helix chain 'F' and resid 558 through 568 removed outlier: 3.514A pdb=" N LEU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.552A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.434A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.552A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.434A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC2, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.553A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.435A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AD3, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1707 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: 5.21 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3943 1.33 - 1.46: 4744 1.46 - 1.60: 6871 1.60 - 1.74: 15 1.74 - 1.88: 132 Bond restraints: 15705 Sorted by residual: bond pdb=" CG GLN D 540 " pdb=" CD GLN D 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.61e+01 bond pdb=" CG GLN B 540 " pdb=" CD GLN B 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.61e+01 bond pdb=" CG GLN F 540 " pdb=" CD GLN F 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.60e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.41e+01 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 16106 1.76 - 3.53: 4175 3.53 - 5.29: 814 5.29 - 7.06: 199 7.06 - 8.82: 24 Bond angle restraints: 21318 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 128.38 -8.82 1.01e+00 9.80e-01 7.63e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.37 -8.81 1.01e+00 9.80e-01 7.61e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.37 -8.50 1.04e+00 9.25e-01 6.67e+01 angle pdb=" C ALA B 558 " pdb=" N PRO B 559 " pdb=" CA PRO B 559 " ideal model delta sigma weight residual 119.32 126.46 -7.14 1.14e+00 7.69e-01 3.92e+01 angle pdb=" C ALA D 558 " pdb=" N PRO D 559 " pdb=" CA PRO D 559 " ideal model delta sigma weight residual 119.32 126.46 -7.14 1.14e+00 7.69e-01 3.92e+01 ... (remaining 21313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 10488 21.14 - 42.29: 198 42.29 - 63.43: 54 63.43 - 84.58: 36 84.58 - 105.72: 18 Dihedral angle restraints: 10794 sinusoidal: 5676 harmonic: 5118 Sorted by residual: 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 -126.83 40.83 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.81 40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.80 40.80 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 10791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1621 0.098 - 0.196: 573 0.196 - 0.294: 269 0.294 - 0.392: 159 0.392 - 0.490: 81 Chirality restraints: 2703 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2700 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.218 2.00e-02 2.50e+03 1.82e-01 4.15e+02 pdb=" C7 NAG O 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.303 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C7 NAG X 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.303 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C7 NAG g 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " 0.302 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " 0.011 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 6533 2.91 - 3.41: 14158 3.41 - 3.91: 26517 3.91 - 4.40: 30440 4.40 - 4.90: 45822 Nonbonded interactions: 123470 Sorted by model distance: nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.419 2.496 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.419 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.419 2.496 nonbonded pdb=" NZ LYS A 232 " pdb=" OE1 GLU A 268 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS C 232 " pdb=" OE1 GLU C 268 " model vdw 2.435 3.120 ... (remaining 123465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.250 Process input model: 36.400 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.023 0.128 15705 Z= 1.476 Angle : 1.694 8.821 21318 Z= 1.097 Chirality : 0.156 0.490 2703 Planarity : 0.011 0.182 2583 Dihedral : 11.041 105.720 7368 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1740 helix: 0.27 (0.22), residues: 513 sheet: 0.97 (0.22), residues: 426 loop : 0.98 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.013 TRP E 35 HIS 0.012 0.003 HIS D 564 PHE 0.023 0.006 PHE A 53 TYR 0.038 0.006 TYR C 40 ARG 0.007 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8135 (t0) cc_final: 0.7887 (t0) REVERT: A 426 MET cc_start: 0.7657 (mtp) cc_final: 0.6695 (mtp) REVERT: B 621 GLU cc_start: 0.7915 (tt0) cc_final: 0.7706 (tp30) REVERT: B 647 GLU cc_start: 0.8043 (tt0) cc_final: 0.7434 (tt0) REVERT: C 80 ASN cc_start: 0.7960 (t0) cc_final: 0.7727 (t0) REVERT: C 426 MET cc_start: 0.7631 (mtp) cc_final: 0.6892 (mtp) REVERT: D 603 ILE cc_start: 0.9409 (mt) cc_final: 0.9088 (mt) REVERT: D 621 GLU cc_start: 0.8096 (tt0) cc_final: 0.7613 (tp30) REVERT: D 639 THR cc_start: 0.8747 (m) cc_final: 0.8519 (p) REVERT: E 80 ASN cc_start: 0.8177 (t0) cc_final: 0.7921 (t0) REVERT: E 426 MET cc_start: 0.7197 (mtp) cc_final: 0.6312 (mtp) REVERT: F 570 HIS cc_start: 0.7968 (m170) cc_final: 0.7658 (m-70) REVERT: F 603 ILE cc_start: 0.9436 (mt) cc_final: 0.9135 (mt) REVERT: F 621 GLU cc_start: 0.7979 (tt0) cc_final: 0.7631 (tp30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3232 time to fit residues: 115.4468 Evaluate side-chains 144 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN B 575 GLN B 577 GLN B 625 ASN D 562 GLN D 570 HIS D 575 GLN D 577 GLN F 562 GLN F 575 GLN F 577 GLN F 625 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15705 Z= 0.279 Angle : 0.657 7.453 21318 Z= 0.350 Chirality : 0.047 0.176 2703 Planarity : 0.004 0.026 2583 Dihedral : 7.987 80.678 3999 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.70 % Allowed : 4.36 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1740 helix: 1.57 (0.23), residues: 489 sheet: 0.72 (0.22), residues: 441 loop : 0.55 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 112 HIS 0.005 0.001 HIS A 72 PHE 0.014 0.002 PHE C 176 TYR 0.022 0.002 TYR A 39 ARG 0.004 0.001 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8066 (t0) cc_final: 0.7794 (t0) REVERT: B 655 LYS cc_start: 0.9063 (tptp) cc_final: 0.8769 (pttp) REVERT: C 80 ASN cc_start: 0.7905 (t0) cc_final: 0.7603 (t0) REVERT: D 530 MET cc_start: 0.7721 (mtm) cc_final: 0.7495 (mtp) REVERT: D 566 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8693 (pp) REVERT: D 621 GLU cc_start: 0.8013 (tt0) cc_final: 0.7797 (tp30) REVERT: D 622 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (mm) outliers start: 27 outliers final: 16 residues processed: 182 average time/residue: 0.2716 time to fit residues: 74.0199 Evaluate side-chains 154 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 170 GLN B 625 ASN C 130 GLN C 170 GLN C 478 ASN D 543 ASN D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 170 GLN F 543 ASN F 625 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15705 Z= 0.458 Angle : 0.701 8.977 21318 Z= 0.364 Chirality : 0.047 0.204 2703 Planarity : 0.004 0.033 2583 Dihedral : 7.372 74.164 3999 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.02 % Allowed : 5.49 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1740 helix: 1.96 (0.24), residues: 471 sheet: 0.66 (0.24), residues: 417 loop : 0.26 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.006 0.002 HIS A 105 PHE 0.029 0.002 PHE B 522 TYR 0.020 0.002 TYR F 643 ARG 0.008 0.001 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8348 (t0) cc_final: 0.8136 (t0) REVERT: B 567 LYS cc_start: 0.8094 (pttp) cc_final: 0.7685 (pttm) REVERT: D 603 ILE cc_start: 0.9552 (mt) cc_final: 0.9147 (mp) REVERT: F 567 LYS cc_start: 0.8219 (pttp) cc_final: 0.7874 (pttm) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.2799 time to fit residues: 64.8785 Evaluate side-chains 143 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15705 Z= 0.323 Angle : 0.597 7.311 21318 Z= 0.313 Chirality : 0.044 0.205 2703 Planarity : 0.004 0.027 2583 Dihedral : 6.849 68.175 3999 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.64 % Allowed : 6.25 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1740 helix: 2.10 (0.24), residues: 471 sheet: 0.58 (0.24), residues: 429 loop : 0.14 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 623 HIS 0.006 0.001 HIS F 564 PHE 0.019 0.002 PHE B 522 TYR 0.012 0.001 TYR E 217 ARG 0.008 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 548 ILE cc_start: 0.7705 (mt) cc_final: 0.7496 (tt) REVERT: B 567 LYS cc_start: 0.8180 (pttp) cc_final: 0.7839 (pttp) REVERT: E 355 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7900 (p0) REVERT: E 434 MET cc_start: 0.8847 (ttp) cc_final: 0.8616 (ttp) REVERT: F 567 LYS cc_start: 0.8201 (pttp) cc_final: 0.7925 (pttp) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 0.2915 time to fit residues: 61.4500 Evaluate side-chains 135 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15705 Z= 0.348 Angle : 0.599 8.943 21318 Z= 0.311 Chirality : 0.044 0.218 2703 Planarity : 0.003 0.027 2583 Dihedral : 6.512 61.928 3999 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.70 % Allowed : 6.82 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1740 helix: 2.15 (0.25), residues: 471 sheet: 0.43 (0.23), residues: 459 loop : 0.12 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 112 HIS 0.006 0.001 HIS F 564 PHE 0.010 0.002 PHE C 176 TYR 0.010 0.001 TYR A 177 ARG 0.005 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.813 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 80 ASN cc_start: 0.8235 (t0) cc_final: 0.7869 (p0) REVERT: B 567 LYS cc_start: 0.8189 (pttp) cc_final: 0.7785 (pttp) REVERT: C 104 MET cc_start: 0.8884 (ttm) cc_final: 0.8584 (tpp) REVERT: D 567 LYS cc_start: 0.8206 (pttm) cc_final: 0.7845 (pttm) REVERT: E 95 MET cc_start: 0.8193 (ptp) cc_final: 0.7865 (ptp) REVERT: E 355 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7994 (p0) REVERT: F 567 LYS cc_start: 0.8307 (pttp) cc_final: 0.7954 (pttp) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.3276 time to fit residues: 67.9708 Evaluate side-chains 137 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 162 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15705 Z= 0.231 Angle : 0.543 9.187 21318 Z= 0.287 Chirality : 0.043 0.215 2703 Planarity : 0.003 0.030 2583 Dihedral : 5.972 53.601 3999 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.26 % Allowed : 7.58 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1740 helix: 2.44 (0.25), residues: 471 sheet: 0.35 (0.24), residues: 447 loop : 0.07 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 623 HIS 0.006 0.001 HIS F 564 PHE 0.009 0.001 PHE C 176 TYR 0.008 0.001 TYR C 191 ARG 0.008 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.929 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 80 ASN cc_start: 0.8279 (t0) cc_final: 0.7906 (p0) REVERT: B 567 LYS cc_start: 0.8197 (pttp) cc_final: 0.7793 (pttp) REVERT: C 95 MET cc_start: 0.8401 (ptp) cc_final: 0.8113 (ptp) REVERT: C 104 MET cc_start: 0.8788 (ttm) cc_final: 0.8515 (tpp) REVERT: C 161 MET cc_start: 0.8624 (tpp) cc_final: 0.7964 (tpt) REVERT: D 567 LYS cc_start: 0.8240 (pttm) cc_final: 0.7926 (pttm) REVERT: D 641 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8301 (tp) REVERT: E 95 MET cc_start: 0.8156 (ptp) cc_final: 0.7831 (ptp) REVERT: E 355 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7974 (p0) REVERT: F 567 LYS cc_start: 0.8342 (pttp) cc_final: 0.7959 (pttp) REVERT: F 655 LYS cc_start: 0.9226 (tptp) cc_final: 0.8833 (pttp) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.3298 time to fit residues: 69.3218 Evaluate side-chains 135 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 570 HIS D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15705 Z= 0.237 Angle : 0.557 9.576 21318 Z= 0.293 Chirality : 0.043 0.191 2703 Planarity : 0.003 0.065 2583 Dihedral : 5.631 58.723 3999 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.39 % Allowed : 7.64 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1740 helix: 2.37 (0.25), residues: 471 sheet: 0.50 (0.24), residues: 438 loop : 0.05 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 112 HIS 0.006 0.001 HIS F 564 PHE 0.009 0.001 PHE A 53 TYR 0.008 0.001 TYR C 191 ARG 0.005 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.763 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 80 ASN cc_start: 0.8302 (t0) cc_final: 0.8023 (p0) REVERT: B 567 LYS cc_start: 0.8240 (pttp) cc_final: 0.7808 (pttp) REVERT: B 648 GLU cc_start: 0.8026 (pp20) cc_final: 0.7789 (pp20) REVERT: C 95 MET cc_start: 0.8371 (ptp) cc_final: 0.8051 (ptp) REVERT: C 161 MET cc_start: 0.8644 (tpp) cc_final: 0.7992 (tpt) REVERT: D 567 LYS cc_start: 0.8182 (pttm) cc_final: 0.7875 (pttm) REVERT: D 601 LYS cc_start: 0.8501 (mppt) cc_final: 0.8120 (mppt) REVERT: D 634 GLU cc_start: 0.8957 (tt0) cc_final: 0.8736 (mt-10) REVERT: D 641 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8277 (tp) REVERT: E 95 MET cc_start: 0.8194 (ptp) cc_final: 0.7815 (ptp) REVERT: F 567 LYS cc_start: 0.8402 (pttp) cc_final: 0.7990 (pttp) REVERT: F 621 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7003 (tm-30) REVERT: F 648 GLU cc_start: 0.8012 (pp20) cc_final: 0.7802 (pp20) REVERT: F 655 LYS cc_start: 0.9203 (tptp) cc_final: 0.8820 (pttp) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.2821 time to fit residues: 57.8002 Evaluate side-chains 137 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS E 99 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15705 Z= 0.232 Angle : 0.536 10.093 21318 Z= 0.283 Chirality : 0.043 0.194 2703 Planarity : 0.003 0.031 2583 Dihedral : 4.590 35.925 3999 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.45 % Allowed : 7.95 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1740 helix: 2.33 (0.25), residues: 471 sheet: 0.80 (0.27), residues: 372 loop : 0.04 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS F 564 PHE 0.009 0.001 PHE E 53 TYR 0.009 0.001 TYR C 191 ARG 0.007 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.760 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 80 ASN cc_start: 0.8315 (t0) cc_final: 0.8071 (p0) REVERT: A 426 MET cc_start: 0.7282 (mmt) cc_final: 0.7050 (mmt) REVERT: B 567 LYS cc_start: 0.8297 (pttp) cc_final: 0.7867 (pttp) REVERT: B 584 GLU cc_start: 0.8604 (tt0) cc_final: 0.8208 (tt0) REVERT: B 648 GLU cc_start: 0.8045 (pp20) cc_final: 0.7771 (pp20) REVERT: B 655 LYS cc_start: 0.9234 (tptp) cc_final: 0.8787 (pttp) REVERT: C 95 MET cc_start: 0.8410 (ptp) cc_final: 0.8071 (ptp) REVERT: C 161 MET cc_start: 0.8639 (tpp) cc_final: 0.7992 (tpt) REVERT: D 567 LYS cc_start: 0.8252 (pttm) cc_final: 0.7908 (pttm) REVERT: D 601 LYS cc_start: 0.8515 (mppt) cc_final: 0.8109 (mppt) REVERT: D 634 GLU cc_start: 0.9000 (tt0) cc_final: 0.8759 (mt-10) REVERT: D 641 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8262 (tp) REVERT: D 648 GLU cc_start: 0.7952 (pp20) cc_final: 0.7690 (pp20) REVERT: F 567 LYS cc_start: 0.8389 (pttp) cc_final: 0.7984 (pttp) REVERT: F 621 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7148 (tm-30) REVERT: F 641 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8168 (tp) REVERT: F 648 GLU cc_start: 0.8127 (pp20) cc_final: 0.7876 (pp20) REVERT: F 655 LYS cc_start: 0.9131 (tptp) cc_final: 0.8795 (pttp) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.2910 time to fit residues: 59.7997 Evaluate side-chains 140 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 122 optimal weight: 0.0370 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS E 99 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15705 Z= 0.270 Angle : 0.561 10.355 21318 Z= 0.296 Chirality : 0.043 0.200 2703 Planarity : 0.003 0.028 2583 Dihedral : 4.396 25.737 3999 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.45 % Allowed : 8.02 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1740 helix: 2.32 (0.25), residues: 471 sheet: 0.70 (0.26), residues: 402 loop : 0.07 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 427 HIS 0.006 0.001 HIS F 564 PHE 0.010 0.001 PHE E 53 TYR 0.009 0.001 TYR C 191 ARG 0.005 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8333 (t0) cc_final: 0.8109 (p0) REVERT: A 161 MET cc_start: 0.8802 (tpp) cc_final: 0.8297 (tpt) REVERT: B 567 LYS cc_start: 0.8318 (pttp) cc_final: 0.7902 (pttp) REVERT: B 648 GLU cc_start: 0.8061 (pp20) cc_final: 0.7775 (pp20) REVERT: B 655 LYS cc_start: 0.9189 (tptp) cc_final: 0.8822 (pttp) REVERT: C 95 MET cc_start: 0.8397 (ptp) cc_final: 0.8044 (ptp) REVERT: C 161 MET cc_start: 0.8630 (tpp) cc_final: 0.7978 (tpt) REVERT: D 567 LYS cc_start: 0.8288 (pttm) cc_final: 0.7936 (pttm) REVERT: D 601 LYS cc_start: 0.8531 (mppt) cc_final: 0.8163 (mppt) REVERT: D 634 GLU cc_start: 0.9000 (tt0) cc_final: 0.8760 (mt-10) REVERT: D 641 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8272 (tp) REVERT: D 648 GLU cc_start: 0.7925 (pp20) cc_final: 0.7637 (pp20) REVERT: F 567 LYS cc_start: 0.8333 (pttp) cc_final: 0.7918 (pttp) REVERT: F 621 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7129 (tm-30) REVERT: F 641 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8161 (tp) REVERT: F 648 GLU cc_start: 0.8137 (pp20) cc_final: 0.7814 (pp20) outliers start: 23 outliers final: 18 residues processed: 139 average time/residue: 0.2761 time to fit residues: 57.5771 Evaluate side-chains 141 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15705 Z= 0.164 Angle : 0.522 10.866 21318 Z= 0.278 Chirality : 0.042 0.228 2703 Planarity : 0.003 0.027 2583 Dihedral : 4.234 24.878 3999 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.07 % Allowed : 8.21 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1740 helix: 2.36 (0.25), residues: 471 sheet: 0.84 (0.27), residues: 372 loop : 0.07 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 112 HIS 0.005 0.001 HIS F 564 PHE 0.013 0.001 PHE E 53 TYR 0.009 0.001 TYR C 191 ARG 0.003 0.000 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.954 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 161 MET cc_start: 0.8783 (tpp) cc_final: 0.8236 (tpt) REVERT: B 567 LYS cc_start: 0.8291 (pttp) cc_final: 0.7852 (pttp) REVERT: B 648 GLU cc_start: 0.8000 (pp20) cc_final: 0.7697 (pp20) REVERT: C 95 MET cc_start: 0.8346 (ptp) cc_final: 0.8031 (ptp) REVERT: C 161 MET cc_start: 0.8596 (tpp) cc_final: 0.7956 (tpt) REVERT: D 634 GLU cc_start: 0.8963 (tt0) cc_final: 0.8756 (mt-10) REVERT: D 648 GLU cc_start: 0.7967 (pp20) cc_final: 0.7665 (pp20) REVERT: F 557 ARG cc_start: 0.8481 (tmm160) cc_final: 0.8258 (ttp80) REVERT: F 567 LYS cc_start: 0.8313 (pttp) cc_final: 0.7912 (pttp) REVERT: F 621 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7144 (tm-30) REVERT: F 626 MET cc_start: 0.7779 (ttm) cc_final: 0.7549 (ttm) REVERT: F 641 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8171 (tp) REVERT: F 648 GLU cc_start: 0.8146 (pp20) cc_final: 0.7800 (pp20) REVERT: F 654 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 655 LYS cc_start: 0.9153 (tptp) cc_final: 0.8736 (pttp) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.2997 time to fit residues: 67.4631 Evaluate side-chains 142 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN D 570 HIS E 99 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.052384 restraints weight = 47731.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054611 restraints weight = 26337.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056114 restraints weight = 18533.950| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15705 Z= 0.238 Angle : 0.561 10.585 21318 Z= 0.295 Chirality : 0.043 0.210 2703 Planarity : 0.003 0.027 2583 Dihedral : 4.184 23.811 3999 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.39 % Allowed : 8.71 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1740 helix: 2.27 (0.25), residues: 471 sheet: 0.85 (0.27), residues: 372 loop : 0.08 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 112 HIS 0.005 0.001 HIS F 564 PHE 0.011 0.001 PHE E 53 TYR 0.012 0.001 TYR E 39 ARG 0.003 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.80 seconds wall clock time: 45 minutes 49.05 seconds (2749.05 seconds total)