Starting phenix.real_space_refine on Sun Feb 18 15:40:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/02_2024/8dpl_27637.pdb" } resolution = 2.53 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5541 atoms to isotropic. 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 63 5.16 5 C 10665 2.51 5 N 2835 2.21 5 O 3309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 50": "NH1" <-> "NH2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "K TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 98": "NH1" <-> "NH2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 219": "NH1" <-> "NH2" Residue "I TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 85": "NH1" <-> "NH2" Residue "M PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 219": "NH1" <-> "NH2" Residue "M TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16872 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "J" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "M" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.12, per 1000 atoms: 0.54 Number of scatterers: 16872 At special positions: 0 Unit cell: (129.69, 127.71, 121.77, 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 63 16.00 O 3309 8.00 N 2835 7.00 C 10665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 161 " - pdb=" SG CYS O 226 " distance=2.03 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 121 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 511 " - pdb=" SG CYS J 556 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS M 108 " - pdb=" SG CYS M 135 " distance=2.03 Simple disulfide: pdb=" SG CYS M 121 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS N 511 " - pdb=" SG CYS N 556 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG D 401 " - " ASN D 228 " " NAG I 401 " - " ASN I 228 " " NAG M 401 " - " ASN M 228 " " NAG P 1 " - " ASN J 563 " " NAG Q 1 " - " ASN E 563 " " NAG R 1 " - " ASN N 563 " Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 3.0 seconds 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 9.8% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.600A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.999A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.588A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.006A pdb=" N SER C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.588A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.993A pdb=" N SER O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 74 Processing helix chain 'I' and resid 78 through 84 removed outlier: 3.658A pdb=" N LYS I 84 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 541 Processing helix chain 'J' and resid 551 through 576 removed outlier: 3.670A pdb=" N ILE J 555 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR J 566 " --> pdb=" O ALA J 562 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN J 567 " --> pdb=" O ASN J 563 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA J 568 " --> pdb=" O GLU J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 597 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.696A pdb=" N LYS D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 551 through 576 removed outlier: 3.667A pdb=" N ILE E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'M' and resid 71 through 74 Processing helix chain 'M' and resid 78 through 84 removed outlier: 3.667A pdb=" N LYS M 84 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 541 Processing helix chain 'N' and resid 551 through 576 removed outlier: 3.680A pdb=" N ILE N 555 " --> pdb=" O GLN N 551 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR N 566 " --> pdb=" O ALA N 562 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN N 567 " --> pdb=" O ASN N 563 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA N 568 " --> pdb=" O GLU N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 583 through 597 Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.727A pdb=" N TYR F 102 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP F 107 " --> pdb=" O TYR F 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.718A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.627A pdb=" N VAL H 157 " --> pdb=" O ILE H 213 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR H 207 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N GLN H 165 " --> pdb=" O SER H 205 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER H 205 " --> pdb=" O GLN H 165 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N VAL H 167 " --> pdb=" O SER H 203 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N SER H 203 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 191 through 192 removed outlier: 5.268A pdb=" N LEU H 184 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN H 175 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 186 " --> pdb=" O TRP H 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.895A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.747A pdb=" N TYR A 102 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP A 107 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.748A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.876A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.876A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.620A pdb=" N VAL C 157 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR C 207 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N GLN C 165 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N SER C 205 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N VAL C 167 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N SER C 203 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.634A pdb=" N TRP C 173 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR C 187 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 171 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.887A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.742A pdb=" N TYR K 102 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP K 107 " --> pdb=" O TYR K 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.731A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AD1, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.874A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR O 107 " --> pdb=" O ARG O 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.874A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 142 through 144 removed outlier: 3.623A pdb=" N VAL O 157 " --> pdb=" O ILE O 213 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR O 207 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N GLN O 165 " --> pdb=" O SER O 205 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N SER O 205 " --> pdb=" O GLN O 165 " (cutoff:3.500A) removed outlier: 12.168A pdb=" N VAL O 167 " --> pdb=" O SER O 203 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N SER O 203 " --> pdb=" O VAL O 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 191 through 192 removed outlier: 5.263A pdb=" N LEU O 184 " --> pdb=" O GLN O 175 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN O 175 " --> pdb=" O LEU O 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE O 186 " --> pdb=" O TRP O 173 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 42 through 45 removed outlier: 3.927A pdb=" N ILE I 38 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 42 through 45 removed outlier: 3.927A pdb=" N ILE I 38 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL I 96 " --> pdb=" O THR J 581 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AE1, first strand: chain 'I' and resid 102 through 103 removed outlier: 3.540A pdb=" N LEU J 515 " --> pdb=" O MET J 548 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 108 through 114 removed outlier: 6.645A pdb=" N CYS I 108 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL I 141 " --> pdb=" O CYS I 108 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN I 110 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY I 143 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU I 112 " --> pdb=" O GLY I 143 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.920A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.920A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AE6, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.534A pdb=" N LEU E 515 " --> pdb=" O MET E 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 108 through 114 removed outlier: 6.648A pdb=" N CYS D 108 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 141 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN D 110 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY D 143 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU D 112 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 42 through 45 removed outlier: 3.917A pdb=" N ILE M 38 " --> pdb=" O ILE M 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 42 through 45 removed outlier: 3.917A pdb=" N ILE M 38 " --> pdb=" O ILE M 185 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL M 96 " --> pdb=" O THR N 581 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 86 through 89 Processing sheet with id=AF2, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.536A pdb=" N LEU N 515 " --> pdb=" O MET N 548 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 108 through 114 removed outlier: 6.641A pdb=" N CYS M 108 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL M 141 " --> pdb=" O CYS M 108 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN M 110 " --> pdb=" O VAL M 141 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY M 143 " --> pdb=" O ASN M 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU M 112 " --> pdb=" O GLY M 143 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1623 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: 6.11 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5358 1.34 - 1.46: 4264 1.46 - 1.58: 7568 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 17271 Sorted by residual: bond pdb=" C1 MAN P 6 " pdb=" C2 MAN P 6 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN R 6 " pdb=" C2 MAN R 6 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 MAN Q 6 " pdb=" C2 MAN Q 6 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 17266 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.41: 600 107.41 - 114.06: 9626 114.06 - 120.71: 6645 120.71 - 127.37: 6379 127.37 - 134.02: 213 Bond angle restraints: 23463 Sorted by residual: angle pdb=" C TYR O 230 " pdb=" N SER O 231 " pdb=" CA SER O 231 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.41e+00 angle pdb=" N SER C 231 " pdb=" CA SER C 231 " pdb=" CB SER C 231 " ideal model delta sigma weight residual 113.65 110.07 3.58 1.47e+00 4.63e-01 5.92e+00 angle pdb=" N SER H 231 " pdb=" CA SER H 231 " pdb=" CB SER H 231 " ideal model delta sigma weight residual 113.65 110.14 3.51 1.47e+00 4.63e-01 5.71e+00 angle pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" O2 MAN R 4 " ideal model delta sigma weight residual 111.77 105.39 6.38 3.00e+00 1.11e-01 4.52e+00 angle pdb=" C3 MAN P 4 " pdb=" C2 MAN P 4 " pdb=" O2 MAN P 4 " ideal model delta sigma weight residual 111.77 105.40 6.37 3.00e+00 1.11e-01 4.50e+00 ... (remaining 23458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 10122 21.63 - 43.26: 177 43.26 - 64.89: 12 64.89 - 86.52: 18 86.52 - 108.16: 12 Dihedral angle restraints: 10341 sinusoidal: 4209 harmonic: 6132 Sorted by residual: dihedral pdb=" CA TYR K 104 " pdb=" C TYR K 104 " pdb=" N ASN K 105 " pdb=" CA ASN K 105 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR F 104 " pdb=" C TYR F 104 " pdb=" N ASN F 105 " pdb=" CA ASN F 105 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR A 104 " pdb=" C TYR A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 10338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2460 0.099 - 0.199: 162 0.199 - 0.298: 3 0.298 - 0.397: 0 0.397 - 0.496: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN J 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN N 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 2625 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 234 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO H 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO O 233 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO O 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO O 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO O 234 " 0.028 5.00e-02 4.00e+02 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4121 2.80 - 3.33: 14026 3.33 - 3.85: 27142 3.85 - 4.38: 33011 4.38 - 4.90: 57882 Nonbonded interactions: 136182 Sorted by model distance: nonbonded pdb=" OE1 GLN H 144 " pdb=" OG1 THR H 241 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLN C 144 " pdb=" OG1 THR C 241 " model vdw 2.281 2.440 nonbonded pdb=" OE1 GLN O 144 " pdb=" OG1 THR O 241 " model vdw 2.285 2.440 nonbonded pdb=" O7 NAG P 2 " pdb=" O4 MAN P 4 " model vdw 2.286 2.440 nonbonded pdb=" O7 NAG R 2 " pdb=" O4 MAN R 4 " model vdw 2.287 2.440 ... (remaining 136177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 7.520 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 46.490 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.002 0.031 17271 Z= 0.144 Angle : 0.482 6.377 23463 Z= 0.250 Chirality : 0.045 0.496 2628 Planarity : 0.003 0.050 2967 Dihedral : 9.406 108.156 6396 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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 (0.19), residues: 2115 helix: 1.16 (0.39), residues: 174 sheet: 1.27 (0.18), residues: 906 loop : 0.28 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 47 HIS 0.003 0.001 HIS H 229 PHE 0.005 0.001 PHE M 225 TYR 0.010 0.001 TYR K 106 ARG 0.002 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.8179 (t) cc_final: 0.7914 (t) REVERT: F 106 TYR cc_start: 0.6880 (m-80) cc_final: 0.6559 (m-80) REVERT: K 100 THR cc_start: 0.8034 (t) cc_final: 0.7762 (t) REVERT: L 87 ASP cc_start: 0.8217 (m-30) cc_final: 0.7727 (m-30) REVERT: D 228 ASN cc_start: 0.8380 (p0) cc_final: 0.8048 (p0) outliers start: 0 outliers final: 6 residues processed: 507 average time/residue: 1.4515 time to fit residues: 807.4728 Evaluate side-chains 340 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 334 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain O residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN A 31 ASN L 28 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.076 17271 Z= 0.724 Angle : 0.773 8.598 23463 Z= 0.396 Chirality : 0.050 0.198 2628 Planarity : 0.006 0.054 2967 Dihedral : 9.319 121.909 2775 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.04 % Allowed : 14.25 % Favored : 82.71 % 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: 0.47 (0.18), residues: 2115 helix: 1.47 (0.38), residues: 156 sheet: 0.65 (0.17), residues: 918 loop : -0.09 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 99 HIS 0.010 0.002 HIS H 229 PHE 0.026 0.002 PHE A 97 TYR 0.023 0.002 TYR A 106 ARG 0.010 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 339 time to evaluate : 1.967 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: G 85 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 103 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7425 (ttp80) REVERT: B 85 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 221 MET cc_start: 0.5938 (mmt) cc_final: 0.5545 (mmt) REVERT: L 85 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7846 (mm-30) REVERT: J 523 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: E 523 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6590 (pt0) REVERT: N 523 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6943 (pt0) outliers start: 54 outliers final: 30 residues processed: 361 average time/residue: 1.5378 time to fit residues: 605.5369 Evaluate side-chains 338 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN B 55 ASN K 31 ASN I 44 GLN J 595 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 595 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17271 Z= 0.173 Angle : 0.596 8.183 23463 Z= 0.301 Chirality : 0.043 0.169 2628 Planarity : 0.005 0.056 2967 Dihedral : 8.340 106.692 2767 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.14 % Allowed : 15.54 % Favored : 82.32 % 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: 0.63 (0.18), residues: 2115 helix: 2.08 (0.40), residues: 156 sheet: 0.81 (0.17), residues: 918 loop : -0.14 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS O 229 PHE 0.012 0.001 PHE A 97 TYR 0.015 0.001 TYR F 104 ARG 0.012 0.001 ARG G 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 346 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 75 ASP cc_start: 0.7847 (t0) cc_final: 0.7397 (t0) REVERT: F 103 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.6566 (mtp-110) REVERT: G 85 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 85 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8086 (mm-30) REVERT: C 221 MET cc_start: 0.5874 (mmt) cc_final: 0.5471 (mmt) REVERT: L 85 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7988 (mm-30) REVERT: J 523 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: E 523 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6646 (pt0) outliers start: 38 outliers final: 22 residues processed: 361 average time/residue: 1.5857 time to fit residues: 626.5110 Evaluate side-chains 333 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 105 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17271 Z= 0.272 Angle : 0.614 7.891 23463 Z= 0.308 Chirality : 0.043 0.171 2628 Planarity : 0.005 0.060 2967 Dihedral : 8.346 117.272 2765 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.04 % Allowed : 16.61 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2115 helix: 2.40 (0.41), residues: 156 sheet: 0.83 (0.17), residues: 906 loop : -0.17 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.006 0.001 HIS O 229 PHE 0.012 0.001 PHE K 97 TYR 0.022 0.001 TYR G 51 ARG 0.009 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 ASN cc_start: 0.7153 (p0) cc_final: 0.5423 (p0) REVERT: G 85 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8054 (mm-30) REVERT: H 149 MET cc_start: 0.7824 (mtt) cc_final: 0.7624 (mtt) REVERT: B 85 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8158 (mm-30) REVERT: C 221 MET cc_start: 0.5919 (mmt) cc_final: 0.5482 (mmt) REVERT: K 75 ASP cc_start: 0.8286 (t0) cc_final: 0.7279 (t0) REVERT: J 523 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: E 523 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: N 523 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6354 (pt0) outliers start: 54 outliers final: 32 residues processed: 343 average time/residue: 1.5327 time to fit residues: 574.7730 Evaluate side-chains 340 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 305 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN C 6 GLN K 31 ASN K 105 ASN J 595 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17271 Z= 0.397 Angle : 0.660 8.149 23463 Z= 0.333 Chirality : 0.045 0.174 2628 Planarity : 0.005 0.061 2967 Dihedral : 8.492 119.118 2765 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.49 % Allowed : 16.78 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2115 helix: 2.41 (0.41), residues: 156 sheet: 0.70 (0.17), residues: 906 loop : -0.32 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 47 HIS 0.008 0.001 HIS O 229 PHE 0.015 0.001 PHE A 97 TYR 0.017 0.002 TYR A 106 ARG 0.011 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 321 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 85 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8154 (mm-30) REVERT: C 221 MET cc_start: 0.5966 (mmt) cc_final: 0.5513 (mmt) REVERT: K 103 ARG cc_start: 0.7277 (ttp80) cc_final: 0.6869 (ttp80) REVERT: L 85 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8008 (mm-30) REVERT: J 523 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: E 523 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: N 523 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6250 (pt0) outliers start: 62 outliers final: 35 residues processed: 350 average time/residue: 1.5355 time to fit residues: 586.6598 Evaluate side-chains 339 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17271 Z= 0.192 Angle : 0.640 8.619 23463 Z= 0.320 Chirality : 0.044 0.169 2628 Planarity : 0.005 0.063 2967 Dihedral : 7.753 68.148 2763 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.04 % Allowed : 19.14 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.52 (0.18), residues: 2115 helix: 2.54 (0.41), residues: 156 sheet: 0.72 (0.17), residues: 915 loop : -0.28 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 47 HIS 0.005 0.001 HIS H 229 PHE 0.016 0.001 PHE H 148 TYR 0.025 0.001 TYR G 51 ARG 0.012 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 328 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 ASN cc_start: 0.7490 (p0) cc_final: 0.7267 (p0) REVERT: G 85 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8045 (mm-30) REVERT: A 105 ASN cc_start: 0.7613 (p0) cc_final: 0.6704 (p0) REVERT: B 85 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8224 (mm-30) REVERT: C 221 MET cc_start: 0.5977 (mmt) cc_final: 0.5528 (mmt) REVERT: K 103 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6948 (ttp80) REVERT: L 85 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8008 (mm-30) REVERT: J 523 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: E 523 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: N 523 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6499 (pt0) outliers start: 54 outliers final: 27 residues processed: 353 average time/residue: 1.4597 time to fit residues: 564.7437 Evaluate side-chains 334 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 304 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 93 optimal weight: 0.0970 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17271 Z= 0.311 Angle : 0.661 9.102 23463 Z= 0.330 Chirality : 0.044 0.170 2628 Planarity : 0.005 0.062 2967 Dihedral : 7.901 69.866 2763 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.10 % Allowed : 19.14 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.47 (0.18), residues: 2115 helix: 2.59 (0.42), residues: 156 sheet: 0.67 (0.17), residues: 903 loop : -0.31 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.007 0.001 HIS O 229 PHE 0.013 0.001 PHE A 97 TYR 0.028 0.001 TYR G 51 ARG 0.012 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 316 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 ASN cc_start: 0.7489 (p0) cc_final: 0.7287 (p0) REVERT: G 85 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 76 ASP cc_start: 0.7541 (m-30) cc_final: 0.7282 (OUTLIER) REVERT: A 105 ASN cc_start: 0.7580 (p0) cc_final: 0.7287 (p0) REVERT: C 221 MET cc_start: 0.5985 (mmt) cc_final: 0.5523 (mmt) REVERT: L 85 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7875 (tp30) REVERT: J 523 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: J 593 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9361 (mt) REVERT: E 523 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: M 214 TYR cc_start: 0.6721 (p90) cc_final: 0.6483 (p90) REVERT: N 523 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6935 (pm20) outliers start: 55 outliers final: 35 residues processed: 343 average time/residue: 1.5428 time to fit residues: 578.7896 Evaluate side-chains 342 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 304 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN B 28 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17271 Z= 0.235 Angle : 0.669 9.699 23463 Z= 0.332 Chirality : 0.044 0.169 2628 Planarity : 0.005 0.061 2967 Dihedral : 7.707 66.928 2763 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 20.10 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.52 (0.18), residues: 2115 helix: 2.63 (0.42), residues: 156 sheet: 0.76 (0.18), residues: 834 loop : -0.26 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.006 0.001 HIS O 229 PHE 0.016 0.001 PHE H 148 TYR 0.029 0.001 TYR G 51 ARG 0.013 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 ASN cc_start: 0.7467 (p0) cc_final: 0.6405 (p0) REVERT: G 85 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 105 ASN cc_start: 0.7584 (p0) cc_final: 0.7368 (p0) REVERT: B 85 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8146 (tp30) REVERT: C 221 MET cc_start: 0.5939 (mmt) cc_final: 0.5488 (mmt) REVERT: K 76 ASP cc_start: 0.7731 (m-30) cc_final: 0.7338 (m-30) REVERT: L 85 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8066 (tp30) REVERT: J 523 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: J 593 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9337 (mt) REVERT: E 523 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6728 (pt0) outliers start: 48 outliers final: 29 residues processed: 346 average time/residue: 1.5421 time to fit residues: 583.8474 Evaluate side-chains 339 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN B 28 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN E 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17271 Z= 0.290 Angle : 0.690 10.242 23463 Z= 0.342 Chirality : 0.044 0.168 2628 Planarity : 0.006 0.135 2967 Dihedral : 7.817 67.575 2763 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.42 % Allowed : 20.33 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.50 (0.18), residues: 2115 helix: 2.66 (0.42), residues: 156 sheet: 0.73 (0.18), residues: 831 loop : -0.27 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.007 0.001 HIS O 229 PHE 0.012 0.001 PHE A 97 TYR 0.029 0.001 TYR G 51 ARG 0.016 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 318 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 89 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8483 (mmtt) REVERT: A 92 ASP cc_start: 0.8867 (m-30) cc_final: 0.8587 (m-30) REVERT: B 85 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8073 (tp30) REVERT: B 111 VAL cc_start: 0.8101 (t) cc_final: 0.7846 (p) REVERT: C 221 MET cc_start: 0.5951 (mmt) cc_final: 0.5496 (mmt) REVERT: I 54 ARG cc_start: 0.7596 (ppt170) cc_final: 0.7287 (pmt170) REVERT: J 523 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: J 593 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9345 (mt) REVERT: E 523 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6785 (pt0) outliers start: 43 outliers final: 30 residues processed: 341 average time/residue: 1.5184 time to fit residues: 566.0106 Evaluate side-chains 345 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 312 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN B 28 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17271 Z= 0.329 Angle : 0.723 10.455 23463 Z= 0.359 Chirality : 0.045 0.167 2628 Planarity : 0.005 0.067 2967 Dihedral : 7.881 68.090 2763 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.31 % Allowed : 20.55 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.46 (0.18), residues: 2115 helix: 2.69 (0.43), residues: 156 sheet: 0.71 (0.18), residues: 831 loop : -0.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.007 0.001 HIS O 229 PHE 0.016 0.001 PHE H 148 TYR 0.031 0.001 TYR G 51 ARG 0.016 0.001 ARG O 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 322 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8072 (mm-30) REVERT: G 98 ARG cc_start: 0.7218 (mmp80) cc_final: 0.6744 (mmp80) REVERT: A 89 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8482 (mmtt) REVERT: A 92 ASP cc_start: 0.8880 (m-30) cc_final: 0.8602 (m-30) REVERT: B 85 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8071 (tp30) REVERT: B 111 VAL cc_start: 0.8180 (t) cc_final: 0.7961 (p) REVERT: C 221 MET cc_start: 0.5959 (mmt) cc_final: 0.5487 (mmt) REVERT: L 85 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8079 (mm-30) REVERT: L 98 ARG cc_start: 0.7619 (mmp80) cc_final: 0.7156 (mmp80) REVERT: I 231 GLU cc_start: 0.6315 (pm20) cc_final: 0.6069 (pm20) REVERT: J 523 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: J 593 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9351 (mt) REVERT: E 523 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6857 (pt0) outliers start: 41 outliers final: 32 residues processed: 344 average time/residue: 1.5518 time to fit residues: 584.6313 Evaluate side-chains 349 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 314 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 552 ASP Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 552 ASP Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN E 595 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.044887 restraints weight = 45625.543| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.54 r_work: 0.2542 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17271 Z= 0.267 Angle : 0.706 11.441 23463 Z= 0.349 Chirality : 0.044 0.166 2628 Planarity : 0.005 0.074 2967 Dihedral : 7.730 65.990 2763 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.20 % Allowed : 20.95 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.48 (0.18), residues: 2115 helix: 2.71 (0.42), residues: 156 sheet: 0.74 (0.18), residues: 831 loop : -0.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS O 229 PHE 0.011 0.001 PHE A 97 TYR 0.030 0.001 TYR G 51 ARG 0.016 0.001 ARG C 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8649.30 seconds wall clock time: 153 minutes 11.98 seconds (9191.98 seconds total)