Starting phenix.real_space_refine on Sat Jul 4 14:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpl_27637/07_2026/8dpl_27637.map" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 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: 1.46 Conformation dependent library (CDL) restraints added in 878.4 milliseconds 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: 0.64 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: 3.24 Time building geometry restraints manager: 1.93 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: 0.00 - 1.28: 22897 1.28 - 2.55: 406 2.55 - 3.83: 104 3.83 - 5.10: 41 5.10 - 6.38: 15 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 - 10.91: 9343 10.91 - 21.83: 408 21.83 - 32.74: 128 32.74 - 43.66: 34 43.66 - 54.57: 11 Dihedral angle restraints: 9924 sinusoidal: 3792 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 9921 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 3.040 nonbonded pdb=" OE1 GLN C 144 " pdb=" OG1 THR C 241 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN O 144 " pdb=" OG1 THR O 241 " model vdw 2.285 3.040 nonbonded pdb=" O7 NAG P 2 " pdb=" O4 MAN P 4 " model vdw 2.286 3.040 nonbonded pdb=" O7 NAG R 2 " pdb=" O4 MAN R 4 " model vdw 2.287 3.040 ... (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 Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'E' 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 17313 Z= 0.114 Angle : 0.511 9.850 23568 Z= 0.256 Chirality : 0.045 0.496 2628 Planarity : 0.003 0.050 2967 Dihedral : 7.105 54.571 5979 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG H 54 TYR 0.010 0.001 TYR K 106 PHE 0.005 0.001 PHE M 225 TRP 0.006 0.001 TRP F 47 HIS 0.003 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (17271) covalent geometry : angle 0.48228 / 0.25 (23463) SS BOND : bond 0.00171 / 0.12 ( 21) SS BOND : angle 0.55133 / 0.37 ( 42) hydrogen bonds : bond 0.21641 / 14.74 ( 572) hydrogen bonds : angle 7.24599 / 5.01 ( 1623) link_ALPHA1-3 : bond 0.00438 / 0.23 ( 6) link_ALPHA1-3 : angle 1.46813 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00394 / 0.18 ( 3) link_ALPHA1-6 : angle 1.44379 / 0.75 ( 9) link_BETA1-4 : bond 0.00519 / 0.28 ( 6) link_BETA1-4 : angle 2.23550 / 1.19 ( 18) link_NAG-ASN : bond 0.00271 / 0.16 ( 6) link_NAG-ASN : angle 5.41568 / 3.26 ( 18) *********************** 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 to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 0.649 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: 0.7123 time to fit residues: 398.3226 Evaluate side-chains 340 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN A 3 GLN A 31 ASN C 6 GLN L 28 ASN O 6 GLN I 44 GLN D 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.045529 restraints weight = 45583.067| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.52 r_work: 0.2547 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17313 Z= 0.270 Angle : 0.664 7.269 23568 Z= 0.337 Chirality : 0.046 0.175 2628 Planarity : 0.005 0.052 2967 Dihedral : 4.688 92.002 2358 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.31 % Allowed : 13.91 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2115 helix: 1.79 (0.38), residues: 156 sheet: 0.89 (0.17), residues: 918 loop : 0.22 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.014 0.002 TYR A 104 PHE 0.019 0.002 PHE F 97 TRP 0.012 0.002 TRP K 47 HIS 0.008 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (17271) covalent geometry : angle 0.65470 / 0.33 (23463) SS BOND : bond 0.00638 / 0.46 ( 21) SS BOND : angle 0.95455 / 0.63 ( 42) hydrogen bonds : bond 0.03960 / 2.61 ( 572) hydrogen bonds : angle 5.04454 / 3.54 ( 1623) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 6) link_ALPHA1-3 : angle 1.56791 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00049 / 0.02 ( 3) link_ALPHA1-6 : angle 2.05714 / 1.08 ( 9) link_BETA1-4 : bond 0.00086 / 0.04 ( 6) link_BETA1-4 : angle 3.08955 / 1.64 ( 18) link_NAG-ASN : bond 0.00395 / 0.28 ( 6) link_NAG-ASN : angle 1.71253 / 1.04 ( 18) *********************** 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 388 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8329 (tt0) cc_final: 0.8032 (tt0) REVERT: F 75 ASP cc_start: 0.8458 (t0) cc_final: 0.7937 (t0) REVERT: F 82 TYR cc_start: 0.9065 (m-80) cc_final: 0.8862 (m-80) REVERT: F 103 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8079 (ttp80) REVERT: G 17 ARG cc_start: 0.9142 (mtp-110) cc_final: 0.8563 (ttp80) REVERT: G 85 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8190 (mm-30) REVERT: G 94 ASP cc_start: 0.8331 (t0) cc_final: 0.8121 (t70) REVERT: H 40 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8521 (mmm160) REVERT: H 46 GLU cc_start: 0.8286 (mp0) cc_final: 0.7811 (mp0) REVERT: H 59 ASP cc_start: 0.8674 (t0) cc_final: 0.8289 (t0) REVERT: H 73 ASP cc_start: 0.8588 (t0) cc_final: 0.8362 (t0) REVERT: H 220 ASP cc_start: 0.9053 (m-30) cc_final: 0.8798 (m-30) REVERT: A 103 ARG cc_start: 0.8948 (mtp-110) cc_final: 0.8176 (tmm-80) REVERT: B 85 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 40 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8447 (mmm160) REVERT: C 46 GLU cc_start: 0.8392 (mp0) cc_final: 0.8039 (mp0) REVERT: C 220 ASP cc_start: 0.9171 (m-30) cc_final: 0.8824 (m-30) REVERT: C 221 MET cc_start: 0.6369 (mmt) cc_final: 0.5684 (mmt) REVERT: K 46 GLU cc_start: 0.8605 (tt0) cc_final: 0.8130 (tt0) REVERT: K 82 TYR cc_start: 0.8959 (m-80) cc_final: 0.8724 (m-80) REVERT: K 103 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8817 (mtp-110) REVERT: L 94 ASP cc_start: 0.7994 (t0) cc_final: 0.7737 (t70) REVERT: L 98 ARG cc_start: 0.8896 (mpp80) cc_final: 0.8620 (mmp80) REVERT: O 40 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8548 (mtp-110) REVERT: O 46 GLU cc_start: 0.8407 (mp0) cc_final: 0.7939 (mp0) REVERT: O 220 ASP cc_start: 0.9067 (m-30) cc_final: 0.8867 (m-30) REVERT: I 100 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8688 (mt-10) REVERT: I 228 ASN cc_start: 0.8565 (p0) cc_final: 0.8348 (p0) REVERT: I 231 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7639 (mt-10) REVERT: J 523 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: J 595 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8663 (tt0) REVERT: D 56 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (mmmt) REVERT: D 112 GLU cc_start: 0.8013 (mp0) cc_final: 0.7774 (mp0) REVERT: D 228 ASN cc_start: 0.8244 (p0) cc_final: 0.8012 (p0) REVERT: E 523 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: M 112 GLU cc_start: 0.8170 (mp0) cc_final: 0.7905 (mp0) REVERT: M 136 ARG cc_start: 0.8477 (tpt90) cc_final: 0.7062 (tpm170) REVERT: M 178 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9060 (mt-10) REVERT: M 231 GLU cc_start: 0.7722 (mt-10) cc_final: 0.6676 (mt-10) REVERT: N 523 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: N 540 GLU cc_start: 0.9128 (mp0) cc_final: 0.8923 (pm20) REVERT: N 595 GLN cc_start: 0.8981 (tp40) cc_final: 0.8560 (tt0) outliers start: 41 outliers final: 20 residues processed: 365 average time/residue: 0.7397 time to fit residues: 294.5106 Evaluate side-chains 344 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 318 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 THR 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 I residue 55 ASP 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 56 LYS 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 576 THR 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 576 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN I 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046531 restraints weight = 45848.270| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.52 r_work: 0.2572 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17313 Z= 0.134 Angle : 0.603 8.103 23568 Z= 0.302 Chirality : 0.043 0.169 2628 Planarity : 0.004 0.055 2967 Dihedral : 4.134 27.500 2348 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.80 % Allowed : 14.64 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2115 helix: 2.25 (0.39), residues: 156 sheet: 0.88 (0.17), residues: 924 loop : 0.11 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 587 TYR 0.014 0.001 TYR B 51 PHE 0.012 0.001 PHE H 148 TRP 0.010 0.001 TRP F 47 HIS 0.004 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (17271) covalent geometry : angle 0.59481 / 0.30 (23463) SS BOND : bond 0.00331 / 0.24 ( 21) SS BOND : angle 0.64589 / 0.40 ( 42) hydrogen bonds : bond 0.03071 / 1.97 ( 572) hydrogen bonds : angle 4.53461 / 3.19 ( 1623) link_ALPHA1-3 : bond 0.00432 / 0.24 ( 6) link_ALPHA1-3 : angle 1.37083 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00226 / 0.11 ( 3) link_ALPHA1-6 : angle 1.82101 / 0.99 ( 9) link_BETA1-4 : bond 0.00402 / 0.21 ( 6) link_BETA1-4 : angle 2.68907 / 1.44 ( 18) link_NAG-ASN : bond 0.00272 / 0.15 ( 6) link_NAG-ASN : angle 1.67086 / 0.99 ( 18) *********************** 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 389 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 357 time to evaluate : 0.640 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: F 43 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8898 (mmmm) REVERT: F 46 GLU cc_start: 0.8335 (tt0) cc_final: 0.8094 (tt0) REVERT: F 75 ASP cc_start: 0.8499 (t0) cc_final: 0.7969 (t0) REVERT: F 82 TYR cc_start: 0.9105 (m-80) cc_final: 0.8868 (m-80) REVERT: F 92 ASP cc_start: 0.9235 (m-30) cc_final: 0.8661 (m-30) REVERT: F 103 ARG cc_start: 0.9048 (mtp-110) cc_final: 0.8687 (ttp80) REVERT: F 105 ASN cc_start: 0.8916 (m110) cc_final: 0.8626 (m-40) REVERT: G 85 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8215 (mm-30) REVERT: G 98 ARG cc_start: 0.8928 (mpp80) cc_final: 0.8705 (mpp80) REVERT: H 46 GLU cc_start: 0.8382 (mp0) cc_final: 0.7970 (mp0) REVERT: H 59 ASP cc_start: 0.8713 (t0) cc_final: 0.8296 (t0) REVERT: H 220 ASP cc_start: 0.9181 (m-30) cc_final: 0.8790 (m-30) REVERT: A 43 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8931 (mmmm) REVERT: A 105 ASN cc_start: 0.8889 (m110) cc_final: 0.8499 (p0) REVERT: B 85 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 109 LEU cc_start: 0.8834 (tp) cc_final: 0.8520 (tm) REVERT: C 40 ARG cc_start: 0.8723 (mmm160) cc_final: 0.8434 (mmm160) REVERT: C 46 GLU cc_start: 0.8460 (mp0) cc_final: 0.8048 (mp0) REVERT: C 220 ASP cc_start: 0.9243 (m-30) cc_final: 0.8780 (m-30) REVERT: C 221 MET cc_start: 0.6252 (mmt) cc_final: 0.5486 (mmt) REVERT: K 43 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8837 (mmmm) REVERT: K 46 GLU cc_start: 0.8608 (tt0) cc_final: 0.8129 (tt0) REVERT: K 75 ASP cc_start: 0.8311 (t0) cc_final: 0.7787 (t0) REVERT: K 82 TYR cc_start: 0.8990 (m-80) cc_final: 0.8742 (m-80) REVERT: K 92 ASP cc_start: 0.9183 (m-30) cc_final: 0.8664 (m-30) REVERT: K 104 TYR cc_start: 0.8263 (m-80) cc_final: 0.8056 (m-80) REVERT: K 107 ASP cc_start: 0.8844 (m-30) cc_final: 0.8420 (p0) REVERT: L 85 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8516 (mm-30) REVERT: O 40 ARG cc_start: 0.8827 (mmm160) cc_final: 0.8519 (mmm160) REVERT: O 46 GLU cc_start: 0.8441 (mp0) cc_final: 0.7994 (mp0) REVERT: O 220 ASP cc_start: 0.9232 (m-30) cc_final: 0.8864 (m-30) REVERT: J 523 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: J 544 THR cc_start: 0.9375 (m) cc_final: 0.9091 (p) REVERT: J 595 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8643 (tt0) REVERT: D 112 GLU cc_start: 0.8092 (mp0) cc_final: 0.7813 (mp0) REVERT: D 228 ASN cc_start: 0.8368 (p0) cc_final: 0.8167 (p0) REVERT: E 523 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: M 100 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8648 (pt0) REVERT: M 106 GLU cc_start: 0.8743 (tp30) cc_final: 0.8485 (tp30) REVERT: M 112 GLU cc_start: 0.8240 (mp0) cc_final: 0.7929 (mp0) REVERT: M 214 TYR cc_start: 0.7859 (p90) cc_final: 0.7557 (p90) REVERT: M 231 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7519 (mt-10) REVERT: N 540 GLU cc_start: 0.9128 (mp0) cc_final: 0.8912 (pm20) outliers start: 32 outliers final: 14 residues processed: 372 average time/residue: 0.7127 time to fit residues: 289.8698 Evaluate side-chains 341 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 325 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 523 GLU 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 M residue 55 ASP Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 47 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN A 105 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN K 31 ASN L 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.041764 restraints weight = 47192.952| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.50 r_work: 0.2437 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.089 17313 Z= 0.554 Angle : 0.829 8.836 23568 Z= 0.419 Chirality : 0.052 0.206 2628 Planarity : 0.006 0.065 2967 Dihedral : 5.035 29.964 2346 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.82 % Allowed : 15.09 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2115 helix: 1.80 (0.40), residues: 156 sheet: 0.46 (0.17), residues: 909 loop : -0.45 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 587 TYR 0.036 0.003 TYR A 106 PHE 0.023 0.002 PHE K 97 TRP 0.022 0.002 TRP O 99 HIS 0.010 0.002 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.55 (17271) covalent geometry : angle 0.81574 / 0.42 (23463) SS BOND : bond 0.00733 / 0.51 ( 21) SS BOND : angle 1.42946 / 0.93 ( 42) hydrogen bonds : bond 0.04222 / 2.76 ( 572) hydrogen bonds : angle 4.93932 / 3.48 ( 1623) link_ALPHA1-3 : bond 0.00315 / 0.20 ( 6) link_ALPHA1-3 : angle 1.63420 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00596 / 0.29 ( 3) link_ALPHA1-6 : angle 2.24924 / 1.18 ( 9) link_BETA1-4 : bond 0.00463 / 0.24 ( 6) link_BETA1-4 : angle 3.89120 / 2.06 ( 18) link_NAG-ASN : bond 0.01154 / 0.58 ( 6) link_NAG-ASN : angle 2.53226 / 1.54 ( 18) *********************** 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 375 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 325 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8504 (tt0) cc_final: 0.8198 (tt0) REVERT: F 75 ASP cc_start: 0.8668 (t0) cc_final: 0.7987 (t0) REVERT: F 82 TYR cc_start: 0.9138 (m-80) cc_final: 0.8937 (m-80) REVERT: F 92 ASP cc_start: 0.9270 (m-30) cc_final: 0.8837 (m-30) REVERT: G 85 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8133 (mm-30) REVERT: G 94 ASP cc_start: 0.8405 (t0) cc_final: 0.8200 (t0) REVERT: H 46 GLU cc_start: 0.8420 (mp0) cc_final: 0.8100 (mp0) REVERT: H 59 ASP cc_start: 0.8873 (t0) cc_final: 0.8266 (t0) REVERT: H 220 ASP cc_start: 0.9173 (m-30) cc_final: 0.8830 (m-30) REVERT: A 92 ASP cc_start: 0.9251 (m-30) cc_final: 0.8764 (m-30) REVERT: A 105 ASN cc_start: 0.8972 (m-40) cc_final: 0.8653 (p0) REVERT: B 85 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8190 (mm-30) REVERT: C 46 GLU cc_start: 0.8608 (mp0) cc_final: 0.8177 (mp0) REVERT: C 220 ASP cc_start: 0.9167 (m-30) cc_final: 0.8681 (m-30) REVERT: C 221 MET cc_start: 0.6405 (mmt) cc_final: 0.5575 (mmt) REVERT: K 46 GLU cc_start: 0.8611 (tt0) cc_final: 0.8167 (tt0) REVERT: K 75 ASP cc_start: 0.8599 (t0) cc_final: 0.7753 (t0) REVERT: K 82 TYR cc_start: 0.9087 (m-80) cc_final: 0.8823 (m-80) REVERT: K 89 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8355 (mmtt) REVERT: K 92 ASP cc_start: 0.9277 (m-30) cc_final: 0.8889 (m-30) REVERT: K 103 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8260 (mtp85) REVERT: K 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8055 (p0) REVERT: L 81 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: L 85 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8510 (mm-30) REVERT: O 46 GLU cc_start: 0.8507 (mp0) cc_final: 0.8043 (mp0) REVERT: O 220 ASP cc_start: 0.9176 (m-30) cc_final: 0.8796 (m-30) REVERT: I 106 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8256 (tp30) REVERT: I 156 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8815 (mm-30) REVERT: J 523 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: D 112 GLU cc_start: 0.8264 (mp0) cc_final: 0.7911 (mp0) REVERT: D 156 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.9090 (mm-30) REVERT: E 523 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: M 106 GLU cc_start: 0.8876 (tp30) cc_final: 0.8575 (tp30) REVERT: M 112 GLU cc_start: 0.8309 (mp0) cc_final: 0.7986 (mp0) REVERT: M 136 ARG cc_start: 0.8661 (tmt-80) cc_final: 0.8381 (tpm-80) REVERT: M 156 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8943 (mm-30) REVERT: M 231 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7557 (mt-10) REVERT: N 523 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7232 (pt0) outliers start: 50 outliers final: 23 residues processed: 349 average time/residue: 0.7394 time to fit residues: 281.8267 Evaluate side-chains 340 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 107 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain K residue 55 THR 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 L residue 81 GLN Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 156 GLU 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 597 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 0.8980 chunk 205 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 105 ASN F 112 GLN G 28 ASN A 112 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.044756 restraints weight = 45398.468| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.48 r_work: 0.2528 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17313 Z= 0.128 Angle : 0.663 8.693 23568 Z= 0.334 Chirality : 0.044 0.203 2628 Planarity : 0.005 0.061 2967 Dihedral : 4.674 32.686 2346 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.03 % Allowed : 16.84 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2115 helix: 2.29 (0.41), residues: 156 sheet: 0.63 (0.17), residues: 927 loop : -0.39 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 156 TYR 0.031 0.001 TYR F 106 PHE 0.010 0.001 PHE K 97 TRP 0.014 0.001 TRP O 99 HIS 0.005 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (17271) covalent geometry : angle 0.65360 / 0.33 (23463) SS BOND : bond 0.00293 / 0.20 ( 21) SS BOND : angle 0.82973 / 0.49 ( 42) hydrogen bonds : bond 0.02876 / 1.85 ( 572) hydrogen bonds : angle 4.47116 / 3.15 ( 1623) link_ALPHA1-3 : bond 0.00248 / 0.12 ( 6) link_ALPHA1-3 : angle 1.44106 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00056 / 0.03 ( 3) link_ALPHA1-6 : angle 2.00076 / 1.05 ( 9) link_BETA1-4 : bond 0.00466 / 0.23 ( 6) link_BETA1-4 : angle 2.96398 / 1.58 ( 18) link_NAG-ASN : bond 0.00282 / 0.13 ( 6) link_NAG-ASN : angle 1.93602 / 1.13 ( 18) *********************** 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 384 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 0.622 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: F 43 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8768 (mmmm) REVERT: F 46 GLU cc_start: 0.8421 (tt0) cc_final: 0.8118 (tt0) REVERT: F 75 ASP cc_start: 0.8625 (t0) cc_final: 0.7589 (t0) REVERT: F 82 TYR cc_start: 0.9141 (m-80) cc_final: 0.8762 (m-80) REVERT: F 89 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8143 (mmtt) REVERT: F 92 ASP cc_start: 0.9301 (m-30) cc_final: 0.8806 (m-30) REVERT: F 105 ASN cc_start: 0.9112 (m110) cc_final: 0.8837 (p0) REVERT: G 85 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8178 (mm-30) REVERT: H 46 GLU cc_start: 0.8449 (mp0) cc_final: 0.7957 (mp0) REVERT: H 59 ASP cc_start: 0.8769 (t0) cc_final: 0.8220 (t0) REVERT: H 220 ASP cc_start: 0.9153 (m-30) cc_final: 0.8786 (m-30) REVERT: A 75 ASP cc_start: 0.8402 (t0) cc_final: 0.7475 (t0) REVERT: A 78 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9324 (ptpp) REVERT: A 89 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8045 (mmtt) REVERT: A 92 ASP cc_start: 0.9227 (m-30) cc_final: 0.8637 (m-30) REVERT: A 105 ASN cc_start: 0.8992 (m-40) cc_final: 0.8560 (p0) REVERT: B 85 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8280 (mm-30) REVERT: B 98 ARG cc_start: 0.8915 (mpp80) cc_final: 0.8510 (mmp80) REVERT: C 46 GLU cc_start: 0.8594 (mp0) cc_final: 0.8155 (mp0) REVERT: C 220 ASP cc_start: 0.9192 (m-30) cc_final: 0.8706 (m-30) REVERT: C 221 MET cc_start: 0.6314 (mmt) cc_final: 0.5544 (mmt) REVERT: K 43 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8784 (mmmm) REVERT: K 46 GLU cc_start: 0.8582 (tt0) cc_final: 0.8132 (tt0) REVERT: K 75 ASP cc_start: 0.8567 (t0) cc_final: 0.7538 (t0) REVERT: K 82 TYR cc_start: 0.9097 (m-80) cc_final: 0.8744 (m-80) REVERT: K 89 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8199 (mmtt) REVERT: K 92 ASP cc_start: 0.9334 (m-30) cc_final: 0.8849 (m-30) REVERT: K 107 ASP cc_start: 0.8750 (m-30) cc_final: 0.8373 (p0) REVERT: L 80 LEU cc_start: 0.9015 (tt) cc_final: 0.8755 (tt) REVERT: L 81 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: L 85 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8568 (mm-30) REVERT: L 98 ARG cc_start: 0.9002 (mpp80) cc_final: 0.8800 (mpp80) REVERT: O 46 GLU cc_start: 0.8457 (mp0) cc_final: 0.7978 (mp0) REVERT: O 220 ASP cc_start: 0.9193 (m-30) cc_final: 0.8824 (m-30) REVERT: J 522 ASP cc_start: 0.8952 (t0) cc_final: 0.8741 (t0) REVERT: J 544 THR cc_start: 0.9454 (m) cc_final: 0.9062 (p) REVERT: J 595 GLN cc_start: 0.9134 (tp40) cc_final: 0.8838 (tt0) REVERT: D 106 GLU cc_start: 0.8839 (tp30) cc_final: 0.8598 (tp30) REVERT: D 112 GLU cc_start: 0.8187 (mp0) cc_final: 0.7868 (mp0) REVERT: E 523 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: M 100 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9010 (pt0) REVERT: M 106 GLU cc_start: 0.8883 (tp30) cc_final: 0.8626 (tp30) REVERT: M 112 GLU cc_start: 0.8305 (mp0) cc_final: 0.7995 (mp0) REVERT: N 595 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8709 (tt0) outliers start: 36 outliers final: 20 residues processed: 364 average time/residue: 0.7487 time to fit residues: 297.7979 Evaluate side-chains 344 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU 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 106 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.044295 restraints weight = 45620.011| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.52 r_work: 0.2523 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17313 Z= 0.158 Angle : 0.662 8.808 23568 Z= 0.334 Chirality : 0.044 0.172 2628 Planarity : 0.005 0.064 2967 Dihedral : 4.563 31.227 2346 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.91 % Allowed : 17.74 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2115 helix: 2.47 (0.42), residues: 156 sheet: 0.66 (0.17), residues: 912 loop : -0.40 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 587 TYR 0.018 0.001 TYR K 106 PHE 0.015 0.001 PHE H 148 TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS O 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (17271) covalent geometry : angle 0.65286 / 0.33 (23463) SS BOND : bond 0.00330 / 0.23 ( 21) SS BOND : angle 0.86365 / 0.52 ( 42) hydrogen bonds : bond 0.02827 / 1.80 ( 572) hydrogen bonds : angle 4.33598 / 3.06 ( 1623) link_ALPHA1-3 : bond 0.00237 / 0.12 ( 6) link_ALPHA1-3 : angle 1.41770 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00041 / 0.02 ( 3) link_ALPHA1-6 : angle 1.92582 / 1.01 ( 9) link_BETA1-4 : bond 0.00381 / 0.19 ( 6) link_BETA1-4 : angle 2.94900 / 1.56 ( 18) link_NAG-ASN : bond 0.00178 / 0.09 ( 6) link_NAG-ASN : angle 1.83927 / 1.09 ( 18) *********************** 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 370 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 0.665 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: F 46 GLU cc_start: 0.8445 (tt0) cc_final: 0.8102 (tt0) REVERT: F 75 ASP cc_start: 0.8726 (t0) cc_final: 0.7907 (t0) REVERT: F 78 LYS cc_start: 0.9496 (mtmm) cc_final: 0.9175 (mtmm) REVERT: F 89 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8044 (mmtt) REVERT: F 92 ASP cc_start: 0.9316 (m-30) cc_final: 0.8836 (m-30) REVERT: G 85 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8189 (mm-30) REVERT: G 94 ASP cc_start: 0.8343 (t70) cc_final: 0.8128 (t0) REVERT: H 46 GLU cc_start: 0.8462 (mp0) cc_final: 0.8053 (mp0) REVERT: H 59 ASP cc_start: 0.8797 (t0) cc_final: 0.8270 (t0) REVERT: H 220 ASP cc_start: 0.9136 (m-30) cc_final: 0.8803 (m-30) REVERT: A 43 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8742 (mmmm) REVERT: A 75 ASP cc_start: 0.8607 (t0) cc_final: 0.8099 (t0) REVERT: A 92 ASP cc_start: 0.9160 (m-30) cc_final: 0.8730 (m-30) REVERT: A 105 ASN cc_start: 0.9065 (m-40) cc_final: 0.8671 (p0) REVERT: B 85 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8449 (mm-30) REVERT: C 46 GLU cc_start: 0.8619 (mp0) cc_final: 0.8247 (mp0) REVERT: C 59 ASP cc_start: 0.8744 (t0) cc_final: 0.8511 (t0) REVERT: C 220 ASP cc_start: 0.9176 (m-30) cc_final: 0.8735 (m-30) REVERT: C 221 MET cc_start: 0.6316 (mmt) cc_final: 0.5547 (mmt) REVERT: K 43 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8771 (mmmm) REVERT: K 46 GLU cc_start: 0.8580 (tt0) cc_final: 0.8139 (tt0) REVERT: K 75 ASP cc_start: 0.8617 (t0) cc_final: 0.8019 (t0) REVERT: K 82 TYR cc_start: 0.9118 (m-80) cc_final: 0.8854 (m-80) REVERT: K 89 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8254 (mmtp) REVERT: K 92 ASP cc_start: 0.9339 (m-30) cc_final: 0.8905 (m-30) REVERT: K 107 ASP cc_start: 0.8676 (m-30) cc_final: 0.8327 (p0) REVERT: L 81 GLN cc_start: 0.8955 (mp10) cc_final: 0.8733 (mp10) REVERT: L 85 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8535 (mm-30) REVERT: L 98 ARG cc_start: 0.8887 (mpp80) cc_final: 0.8640 (mmp80) REVERT: O 46 GLU cc_start: 0.8500 (mp0) cc_final: 0.8022 (mp0) REVERT: O 156 ARG cc_start: 0.9450 (mtp-110) cc_final: 0.9149 (ttm110) REVERT: O 220 ASP cc_start: 0.9202 (m-30) cc_final: 0.8797 (m-30) REVERT: I 100 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8494 (pt0) REVERT: J 544 THR cc_start: 0.9448 (m) cc_final: 0.9061 (p) REVERT: J 595 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8801 (tt0) REVERT: D 106 GLU cc_start: 0.8899 (tp30) cc_final: 0.8655 (tp30) REVERT: D 112 GLU cc_start: 0.8167 (mp0) cc_final: 0.7833 (mp0) REVERT: E 523 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: M 100 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9026 (pt0) REVERT: M 106 GLU cc_start: 0.8854 (tp30) cc_final: 0.8632 (tp30) REVERT: M 112 GLU cc_start: 0.8300 (mp0) cc_final: 0.7992 (mp0) REVERT: N 595 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8692 (tt0) outliers start: 34 outliers final: 25 residues processed: 352 average time/residue: 0.7256 time to fit residues: 279.4915 Evaluate side-chains 351 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 325 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 TYR 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 103 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 0.3980 chunk 188 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.044267 restraints weight = 45363.619| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.52 r_work: 0.2526 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17313 Z= 0.168 Angle : 0.679 9.305 23568 Z= 0.341 Chirality : 0.044 0.172 2628 Planarity : 0.005 0.064 2967 Dihedral : 4.523 30.640 2346 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.31 % Allowed : 17.91 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2115 helix: 2.55 (0.42), residues: 156 sheet: 0.68 (0.17), residues: 906 loop : -0.38 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 156 TYR 0.026 0.001 TYR G 51 PHE 0.010 0.001 PHE K 97 TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17271) covalent geometry : angle 0.67021 / 0.34 (23463) SS BOND : bond 0.00349 / 0.25 ( 21) SS BOND : angle 0.86327 / 0.53 ( 42) hydrogen bonds : bond 0.02790 / 1.77 ( 572) hydrogen bonds : angle 4.29168 / 3.02 ( 1623) link_ALPHA1-3 : bond 0.00235 / 0.12 ( 6) link_ALPHA1-3 : angle 1.43214 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00073 / 0.04 ( 3) link_ALPHA1-6 : angle 1.90359 / 1.00 ( 9) link_BETA1-4 : bond 0.00377 / 0.18 ( 6) link_BETA1-4 : angle 2.96606 / 1.58 ( 18) link_NAG-ASN : bond 0.00179 / 0.09 ( 6) link_NAG-ASN : angle 1.81834 / 1.08 ( 18) *********************** 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 372 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 0.694 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: F 46 GLU cc_start: 0.8479 (tt0) cc_final: 0.8129 (tt0) REVERT: F 54 LYS cc_start: 0.9519 (tppp) cc_final: 0.9300 (tppt) REVERT: F 75 ASP cc_start: 0.8769 (t0) cc_final: 0.8374 (t0) REVERT: F 89 LYS cc_start: 0.8243 (mmtp) cc_final: 0.8006 (mmtp) REVERT: F 92 ASP cc_start: 0.9281 (m-30) cc_final: 0.8823 (m-30) REVERT: G 85 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8140 (mm-30) REVERT: G 98 ARG cc_start: 0.8865 (mpp80) cc_final: 0.8555 (mmp80) REVERT: H 46 GLU cc_start: 0.8484 (mp0) cc_final: 0.8057 (mp0) REVERT: H 59 ASP cc_start: 0.8796 (t0) cc_final: 0.8298 (t0) REVERT: H 220 ASP cc_start: 0.9141 (m-30) cc_final: 0.8810 (m-30) REVERT: A 43 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8710 (mmmm) REVERT: A 54 LYS cc_start: 0.9470 (tppt) cc_final: 0.9189 (mppt) REVERT: A 75 ASP cc_start: 0.8544 (t0) cc_final: 0.7504 (t0) REVERT: A 78 LYS cc_start: 0.9605 (OUTLIER) cc_final: 0.9370 (ptpp) REVERT: A 89 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8179 (mmtt) REVERT: A 92 ASP cc_start: 0.9183 (m-30) cc_final: 0.8736 (m-30) REVERT: A 105 ASN cc_start: 0.9073 (m-40) cc_final: 0.8689 (p0) REVERT: B 85 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 98 ARG cc_start: 0.8873 (mpp80) cc_final: 0.8452 (mmp80) REVERT: C 46 GLU cc_start: 0.8648 (mp0) cc_final: 0.8289 (mp0) REVERT: C 59 ASP cc_start: 0.8745 (t0) cc_final: 0.8492 (t0) REVERT: C 220 ASP cc_start: 0.9173 (m-30) cc_final: 0.8724 (m-30) REVERT: C 221 MET cc_start: 0.6360 (mmt) cc_final: 0.5560 (mmt) REVERT: K 43 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8733 (mmmm) REVERT: K 46 GLU cc_start: 0.8579 (tt0) cc_final: 0.8139 (tt0) REVERT: K 75 ASP cc_start: 0.8621 (t0) cc_final: 0.7905 (t0) REVERT: K 82 TYR cc_start: 0.9115 (m-80) cc_final: 0.8753 (m-80) REVERT: K 89 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8241 (mmtm) REVERT: K 92 ASP cc_start: 0.9358 (m-30) cc_final: 0.8961 (m-30) REVERT: K 105 ASN cc_start: 0.8879 (m110) cc_final: 0.8664 (m-40) REVERT: K 107 ASP cc_start: 0.8663 (m-30) cc_final: 0.8321 (p0) REVERT: L 85 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8560 (mm-30) REVERT: O 46 GLU cc_start: 0.8484 (mp0) cc_final: 0.8005 (mp0) REVERT: O 220 ASP cc_start: 0.9203 (m-30) cc_final: 0.8821 (m-30) REVERT: I 100 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8350 (pt0) REVERT: J 544 THR cc_start: 0.9448 (m) cc_final: 0.9061 (p) REVERT: J 595 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8807 (tt0) REVERT: D 100 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8871 (pt0) REVERT: D 106 GLU cc_start: 0.8901 (tp30) cc_final: 0.8659 (tp30) REVERT: D 112 GLU cc_start: 0.8148 (mp0) cc_final: 0.7823 (mp0) REVERT: E 523 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: M 100 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9003 (pt0) REVERT: M 106 GLU cc_start: 0.8838 (tp30) cc_final: 0.8595 (tp30) REVERT: M 112 GLU cc_start: 0.8254 (mp0) cc_final: 0.7938 (mp0) REVERT: N 522 ASP cc_start: 0.8885 (t0) cc_final: 0.8685 (t0) REVERT: N 595 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8662 (tt0) outliers start: 41 outliers final: 29 residues processed: 354 average time/residue: 0.7370 time to fit residues: 285.4395 Evaluate side-chains 351 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 TYR 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 103 ARG Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain O residue 104 SER 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 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR 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 152 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 112 GLN A 112 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.045792 restraints weight = 45857.947| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.51 r_work: 0.2559 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17313 Z= 0.128 Angle : 0.681 9.771 23568 Z= 0.340 Chirality : 0.043 0.171 2628 Planarity : 0.005 0.064 2967 Dihedral : 4.435 30.036 2346 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 18.92 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2115 helix: 2.62 (0.41), residues: 156 sheet: 0.80 (0.18), residues: 888 loop : -0.30 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 156 TYR 0.029 0.001 TYR G 51 PHE 0.015 0.001 PHE H 148 TRP 0.011 0.001 TRP K 47 HIS 0.005 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (17271) covalent geometry : angle 0.67372 / 0.34 (23463) SS BOND : bond 0.00293 / 0.21 ( 21) SS BOND : angle 0.71897 / 0.44 ( 42) hydrogen bonds : bond 0.02604 / 1.64 ( 572) hydrogen bonds : angle 4.17762 / 2.94 ( 1623) link_ALPHA1-3 : bond 0.00355 / 0.19 ( 6) link_ALPHA1-3 : angle 1.41005 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00079 / 0.04 ( 3) link_ALPHA1-6 : angle 1.80231 / 0.95 ( 9) link_BETA1-4 : bond 0.00505 / 0.25 ( 6) link_BETA1-4 : angle 2.76474 / 1.47 ( 18) link_NAG-ASN : bond 0.00260 / 0.12 ( 6) link_NAG-ASN : angle 1.68718 / 1.00 ( 18) *********************** 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 368 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 0.668 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: F 46 GLU cc_start: 0.8472 (tt0) cc_final: 0.8012 (tt0) REVERT: F 54 LYS cc_start: 0.9511 (tppp) cc_final: 0.9309 (tppt) REVERT: F 75 ASP cc_start: 0.8796 (t0) cc_final: 0.8427 (t0) REVERT: F 89 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7976 (mmtt) REVERT: F 92 ASP cc_start: 0.9324 (m-30) cc_final: 0.8877 (m-30) REVERT: G 17 ARG cc_start: 0.9173 (mtp-110) cc_final: 0.8919 (mmm160) REVERT: G 68 LYS cc_start: 0.9139 (tttt) cc_final: 0.8861 (tttp) REVERT: G 85 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8183 (mm-30) REVERT: G 98 ARG cc_start: 0.8815 (mpp80) cc_final: 0.8494 (mmp80) REVERT: H 46 GLU cc_start: 0.8488 (mp0) cc_final: 0.8041 (mp0) REVERT: H 59 ASP cc_start: 0.8785 (t0) cc_final: 0.8321 (t0) REVERT: H 220 ASP cc_start: 0.9143 (m-30) cc_final: 0.8884 (m-30) REVERT: A 43 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8665 (mmmm) REVERT: A 54 LYS cc_start: 0.9489 (tppt) cc_final: 0.9199 (mppt) REVERT: A 75 ASP cc_start: 0.8542 (t0) cc_final: 0.7537 (t0) REVERT: A 78 LYS cc_start: 0.9602 (OUTLIER) cc_final: 0.9378 (ptpp) REVERT: A 89 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8115 (mmtt) REVERT: A 92 ASP cc_start: 0.9181 (m-30) cc_final: 0.8764 (m-30) REVERT: A 105 ASN cc_start: 0.9069 (m-40) cc_final: 0.8693 (p0) REVERT: B 85 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 98 ARG cc_start: 0.8783 (mpp80) cc_final: 0.8557 (mmp80) REVERT: C 46 GLU cc_start: 0.8642 (mp0) cc_final: 0.8270 (mp0) REVERT: C 59 ASP cc_start: 0.8746 (t0) cc_final: 0.8476 (t0) REVERT: C 220 ASP cc_start: 0.9188 (m-30) cc_final: 0.8760 (m-30) REVERT: C 221 MET cc_start: 0.6314 (mmt) cc_final: 0.5532 (mmt) REVERT: K 43 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8783 (mmmm) REVERT: K 46 GLU cc_start: 0.8559 (tt0) cc_final: 0.8120 (tt0) REVERT: K 75 ASP cc_start: 0.8657 (t0) cc_final: 0.8000 (t0) REVERT: K 82 TYR cc_start: 0.9133 (m-80) cc_final: 0.8751 (m-80) REVERT: K 89 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8073 (mmtt) REVERT: K 92 ASP cc_start: 0.9365 (m-30) cc_final: 0.8982 (m-30) REVERT: K 105 ASN cc_start: 0.8875 (m110) cc_final: 0.8658 (m-40) REVERT: K 107 ASP cc_start: 0.8656 (m-30) cc_final: 0.8332 (p0) REVERT: L 85 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8498 (mm-30) REVERT: O 46 GLU cc_start: 0.8478 (mp0) cc_final: 0.7993 (mp0) REVERT: O 156 ARG cc_start: 0.9405 (mtp-110) cc_final: 0.9091 (ttm110) REVERT: O 220 ASP cc_start: 0.9233 (m-30) cc_final: 0.8846 (m-30) REVERT: I 100 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8399 (pt0) REVERT: I 136 ARG cc_start: 0.8644 (tpm-80) cc_final: 0.8361 (tpm-80) REVERT: J 523 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: J 544 THR cc_start: 0.9427 (m) cc_final: 0.9064 (p) REVERT: J 595 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8792 (tt0) REVERT: D 100 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8875 (pt0) REVERT: D 106 GLU cc_start: 0.8881 (tp30) cc_final: 0.8613 (tp30) REVERT: D 112 GLU cc_start: 0.8123 (mp0) cc_final: 0.7785 (mp0) REVERT: M 100 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9015 (pt0) REVERT: M 106 GLU cc_start: 0.8831 (tp30) cc_final: 0.8596 (tp30) REVERT: M 112 GLU cc_start: 0.8247 (mp0) cc_final: 0.7920 (mp0) REVERT: M 178 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9064 (mt-10) REVERT: N 522 ASP cc_start: 0.8904 (t0) cc_final: 0.8644 (t0) REVERT: N 595 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8663 (tt0) outliers start: 33 outliers final: 22 residues processed: 352 average time/residue: 0.7404 time to fit residues: 285.0597 Evaluate side-chains 351 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 159 ILE 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 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 576 THR 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 597 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 3.9990 chunk 201 optimal weight: 0.0670 chunk 198 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 28 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.044530 restraints weight = 45775.189| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.54 r_work: 0.2536 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17313 Z= 0.175 Angle : 0.709 10.214 23568 Z= 0.356 Chirality : 0.044 0.171 2628 Planarity : 0.005 0.065 2967 Dihedral : 4.469 29.753 2346 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.86 % Allowed : 19.14 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2115 helix: 2.72 (0.42), residues: 156 sheet: 0.80 (0.18), residues: 852 loop : -0.32 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 156 TYR 0.030 0.001 TYR G 51 PHE 0.011 0.001 PHE A 97 TRP 0.012 0.001 TRP F 47 HIS 0.006 0.001 HIS O 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (17271) covalent geometry : angle 0.70105 / 0.35 (23463) SS BOND : bond 0.00356 / 0.25 ( 21) SS BOND : angle 0.80758 / 0.50 ( 42) hydrogen bonds : bond 0.02754 / 1.73 ( 572) hydrogen bonds : angle 4.19001 / 2.95 ( 1623) link_ALPHA1-3 : bond 0.00214 / 0.12 ( 6) link_ALPHA1-3 : angle 1.43534 / 0.85 ( 18) link_ALPHA1-6 : bond 0.00067 / 0.03 ( 3) link_ALPHA1-6 : angle 1.86080 / 0.98 ( 9) link_BETA1-4 : bond 0.00331 / 0.16 ( 6) link_BETA1-4 : angle 2.93779 / 1.56 ( 18) link_NAG-ASN : bond 0.00149 / 0.07 ( 6) link_NAG-ASN : angle 1.75495 / 1.05 ( 18) *********************** 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 365 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8475 (tt0) cc_final: 0.8126 (tt0) REVERT: F 54 LYS cc_start: 0.9520 (tppp) cc_final: 0.9315 (tppt) REVERT: F 75 ASP cc_start: 0.8766 (t0) cc_final: 0.8370 (t0) REVERT: F 89 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7987 (mmtp) REVERT: F 92 ASP cc_start: 0.9295 (m-30) cc_final: 0.8912 (m-30) REVERT: G 17 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8918 (mmm160) REVERT: G 85 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8195 (mm-30) REVERT: G 98 ARG cc_start: 0.8881 (mpp80) cc_final: 0.8546 (mmp80) REVERT: H 46 GLU cc_start: 0.8511 (mp0) cc_final: 0.8037 (mp0) REVERT: H 59 ASP cc_start: 0.8820 (t0) cc_final: 0.8332 (t0) REVERT: H 220 ASP cc_start: 0.9138 (m-30) cc_final: 0.8853 (m-30) REVERT: A 75 ASP cc_start: 0.8559 (t0) cc_final: 0.7528 (t0) REVERT: A 78 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9380 (ptpp) REVERT: A 89 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8144 (mmtt) REVERT: A 92 ASP cc_start: 0.9171 (m-30) cc_final: 0.8751 (m-30) REVERT: A 105 ASN cc_start: 0.9082 (m-40) cc_final: 0.8675 (p0) REVERT: B 85 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8475 (mm-30) REVERT: B 98 ARG cc_start: 0.8879 (mpp80) cc_final: 0.8520 (mmp80) REVERT: C 46 GLU cc_start: 0.8667 (mp0) cc_final: 0.8291 (mp0) REVERT: C 59 ASP cc_start: 0.8773 (t0) cc_final: 0.8518 (t0) REVERT: C 220 ASP cc_start: 0.9190 (m-30) cc_final: 0.8810 (m-30) REVERT: C 221 MET cc_start: 0.6351 (mmt) cc_final: 0.5554 (mmt) REVERT: K 43 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8797 (mmmm) REVERT: K 46 GLU cc_start: 0.8571 (tt0) cc_final: 0.8136 (tt0) REVERT: K 75 ASP cc_start: 0.8773 (t0) cc_final: 0.8082 (t0) REVERT: K 82 TYR cc_start: 0.9142 (m-80) cc_final: 0.8835 (m-80) REVERT: K 89 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8039 (mmtt) REVERT: K 92 ASP cc_start: 0.9359 (m-30) cc_final: 0.8950 (m-30) REVERT: K 105 ASN cc_start: 0.8879 (m110) cc_final: 0.8662 (m-40) REVERT: K 107 ASP cc_start: 0.8615 (m-30) cc_final: 0.8304 (p0) REVERT: L 85 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8533 (mm-30) REVERT: O 46 GLU cc_start: 0.8495 (mp0) cc_final: 0.8014 (mp0) REVERT: O 156 ARG cc_start: 0.9415 (mtp-110) cc_final: 0.9104 (ttm110) REVERT: O 220 ASP cc_start: 0.9217 (m-30) cc_final: 0.8890 (m-30) REVERT: I 100 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8453 (pt0) REVERT: I 136 ARG cc_start: 0.8660 (tpm-80) cc_final: 0.8387 (tpm-80) REVERT: J 523 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: J 544 THR cc_start: 0.9450 (m) cc_final: 0.9058 (p) REVERT: J 595 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8798 (tt0) REVERT: D 100 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8872 (pt0) REVERT: D 106 GLU cc_start: 0.8882 (tp30) cc_final: 0.8634 (tp30) REVERT: D 112 GLU cc_start: 0.8140 (mp0) cc_final: 0.7801 (mp0) REVERT: D 156 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8868 (mm-30) REVERT: M 100 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9028 (pt0) REVERT: M 106 GLU cc_start: 0.8857 (tp30) cc_final: 0.8598 (tp30) REVERT: M 112 GLU cc_start: 0.8235 (mp0) cc_final: 0.7914 (mp0) REVERT: M 136 ARG cc_start: 0.8633 (tpt90) cc_final: 0.7183 (tpm170) REVERT: M 178 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.9090 (mt-10) REVERT: N 522 ASP cc_start: 0.8926 (t0) cc_final: 0.8653 (t0) REVERT: N 595 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8689 (tt0) outliers start: 33 outliers final: 26 residues processed: 347 average time/residue: 0.7392 time to fit residues: 280.6763 Evaluate side-chains 357 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 328 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 TYR 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 103 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 159 ILE 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 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 597 TRP 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 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 0.0870 chunk 62 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044138 restraints weight = 46088.233| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.48 r_work: 0.2510 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17313 Z= 0.257 Angle : 0.740 10.398 23568 Z= 0.371 Chirality : 0.045 0.171 2628 Planarity : 0.005 0.065 2967 Dihedral : 4.625 30.345 2346 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 19.59 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2115 helix: 2.70 (0.42), residues: 156 sheet: 0.62 (0.17), residues: 897 loop : -0.38 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 587 TYR 0.031 0.002 TYR G 51 PHE 0.016 0.001 PHE H 148 TRP 0.014 0.001 TRP F 47 HIS 0.008 0.001 HIS H 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (17271) covalent geometry : angle 0.73119 / 0.37 (23463) SS BOND : bond 0.00428 / 0.30 ( 21) SS BOND : angle 0.95271 / 0.61 ( 42) hydrogen bonds : bond 0.03024 / 1.92 ( 572) hydrogen bonds : angle 4.31410 / 3.05 ( 1623) link_ALPHA1-3 : bond 0.00153 / 0.08 ( 6) link_ALPHA1-3 : angle 1.48346 / 0.87 ( 18) link_ALPHA1-6 : bond 0.00230 / 0.11 ( 3) link_ALPHA1-6 : angle 1.96182 / 1.03 ( 9) link_BETA1-4 : bond 0.00135 / 0.06 ( 6) link_BETA1-4 : angle 3.19643 / 1.70 ( 18) link_NAG-ASN : bond 0.00087 / 0.03 ( 6) link_NAG-ASN : angle 1.92062 / 1.15 ( 18) ********************** 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 359 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 0.655 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: F 54 LYS cc_start: 0.9540 (tppp) cc_final: 0.9314 (tppt) REVERT: F 75 ASP cc_start: 0.8750 (t0) cc_final: 0.8355 (t0) REVERT: F 88 LEU cc_start: 0.8950 (mm) cc_final: 0.8473 (mm) REVERT: F 92 ASP cc_start: 0.9303 (m-30) cc_final: 0.8953 (m-30) REVERT: F 105 ASN cc_start: 0.9045 (m110) cc_final: 0.8751 (p0) REVERT: G 85 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8138 (mm-30) REVERT: G 98 ARG cc_start: 0.8981 (mpp80) cc_final: 0.8555 (mmp80) REVERT: H 46 GLU cc_start: 0.8544 (mp0) cc_final: 0.8003 (mp0) REVERT: H 59 ASP cc_start: 0.8846 (t0) cc_final: 0.8334 (t0) REVERT: H 220 ASP cc_start: 0.9148 (m-30) cc_final: 0.8905 (m-30) REVERT: A 43 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8768 (mmmm) REVERT: A 54 LYS cc_start: 0.9492 (tppt) cc_final: 0.9238 (mppt) REVERT: A 75 ASP cc_start: 0.8527 (t0) cc_final: 0.7444 (t0) REVERT: A 76 ASP cc_start: 0.8455 (m-30) cc_final: 0.8214 (m-30) REVERT: A 78 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9399 (ptpp) REVERT: A 89 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8139 (mmtt) REVERT: A 92 ASP cc_start: 0.9176 (m-30) cc_final: 0.8729 (m-30) REVERT: A 105 ASN cc_start: 0.9073 (m-40) cc_final: 0.8680 (p0) REVERT: B 85 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 98 ARG cc_start: 0.8977 (mpp80) cc_final: 0.8637 (mmp80) REVERT: C 46 GLU cc_start: 0.8694 (mp0) cc_final: 0.8318 (mp0) REVERT: C 220 ASP cc_start: 0.9187 (m-30) cc_final: 0.8824 (m-30) REVERT: C 221 MET cc_start: 0.6364 (mmt) cc_final: 0.5647 (mmt) REVERT: K 43 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8823 (mmmm) REVERT: K 46 GLU cc_start: 0.8574 (tt0) cc_final: 0.8131 (tt0) REVERT: K 61 ASP cc_start: 0.8561 (p0) cc_final: 0.8090 (p0) REVERT: K 75 ASP cc_start: 0.8834 (t0) cc_final: 0.8229 (t0) REVERT: K 82 TYR cc_start: 0.9173 (m-80) cc_final: 0.8684 (m-80) REVERT: K 89 LYS cc_start: 0.8449 (mmtp) cc_final: 0.8197 (mmtp) REVERT: K 92 ASP cc_start: 0.9351 (m-30) cc_final: 0.8972 (m-30) REVERT: K 105 ASN cc_start: 0.8869 (m110) cc_final: 0.8653 (m-40) REVERT: K 107 ASP cc_start: 0.8583 (m-30) cc_final: 0.8268 (p0) REVERT: L 17 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7624 (ttp80) REVERT: L 85 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8458 (mm-30) REVERT: O 46 GLU cc_start: 0.8503 (mp0) cc_final: 0.8027 (mp0) REVERT: O 156 ARG cc_start: 0.9417 (mtp-110) cc_final: 0.9093 (ttm110) REVERT: I 136 ARG cc_start: 0.8673 (tpm-80) cc_final: 0.8383 (tpm-80) REVERT: J 523 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: J 595 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8836 (tt0) REVERT: D 106 GLU cc_start: 0.8901 (tp30) cc_final: 0.8653 (tp30) REVERT: D 112 GLU cc_start: 0.8136 (mp0) cc_final: 0.7785 (mp0) REVERT: M 100 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9002 (pt0) REVERT: M 106 GLU cc_start: 0.8855 (tp30) cc_final: 0.8602 (tp30) REVERT: M 112 GLU cc_start: 0.8236 (mp0) cc_final: 0.7866 (mp0) REVERT: M 136 ARG cc_start: 0.8649 (tpt90) cc_final: 0.7189 (tpm170) REVERT: N 522 ASP cc_start: 0.8943 (t0) cc_final: 0.8649 (t0) REVERT: N 595 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8715 (tt0) outliers start: 28 outliers final: 21 residues processed: 344 average time/residue: 0.7412 time to fit residues: 278.4968 Evaluate side-chains 350 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 327 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 159 ILE 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 D residue 55 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 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 135 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 28 ASN O 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.045928 restraints weight = 45448.503| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.49 r_work: 0.2566 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17313 Z= 0.129 Angle : 0.717 10.503 23568 Z= 0.358 Chirality : 0.044 0.170 2628 Planarity : 0.005 0.064 2967 Dihedral : 4.452 30.089 2346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.35 % Allowed : 20.27 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2115 helix: 2.73 (0.41), residues: 156 sheet: 0.85 (0.18), residues: 852 loop : -0.37 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 98 TYR 0.030 0.001 TYR G 51 PHE 0.008 0.001 PHE E 592 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS O 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17271) covalent geometry : angle 0.71095 / 0.36 (23463) SS BOND : bond 0.00273 / 0.19 ( 21) SS BOND : angle 0.67056 / 0.40 ( 42) hydrogen bonds : bond 0.02551 / 1.61 ( 572) hydrogen bonds : angle 4.13841 / 2.92 ( 1623) link_ALPHA1-3 : bond 0.00375 / 0.21 ( 6) link_ALPHA1-3 : angle 1.38754 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00121 / 0.05 ( 3) link_ALPHA1-6 : angle 1.74760 / 0.93 ( 9) link_BETA1-4 : bond 0.00567 / 0.29 ( 6) link_BETA1-4 : angle 2.77724 / 1.49 ( 18) link_NAG-ASN : bond 0.00293 / 0.14 ( 6) link_NAG-ASN : angle 1.66183 / 0.98 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7266.94 seconds wall clock time: 124 minutes 30.42 seconds (7470.42 seconds total)