Starting phenix.real_space_refine on Sun Aug 24 16:56:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpl_27637/08_2025/8dpl_27637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpl_27637/08_2025/8dpl_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_27637/08_2025/8dpl_27637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpl_27637/08_2025/8dpl_27637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpl_27637/08_2025/8dpl_27637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpl_27637/08_2025/8dpl_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-2.0-5787/lib/python3.9/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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.09, per 1000 atoms: 0.18 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: 1.26 Conformation dependent library (CDL) restraints added in 568.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.71 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: 2.51 Time building geometry restraints manager: 1.65 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 - 21.63: 10122 21.63 - 43.26: 177 43.26 - 64.89: 12 64.89 - 86.52: 18 86.52 - 108.16: 12 Dihedral angle restraints: 10341 sinusoidal: 4209 harmonic: 6132 Sorted by residual: dihedral pdb=" CA TYR K 104 " pdb=" C TYR K 104 " pdb=" N ASN K 105 " pdb=" CA ASN K 105 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR F 104 " pdb=" C TYR F 104 " pdb=" N ASN F 105 " pdb=" CA ASN F 105 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR A 104 " pdb=" C TYR A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 10338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2460 0.099 - 0.199: 162 0.199 - 0.298: 3 0.298 - 0.397: 0 0.397 - 0.496: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN J 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN N 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 2625 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 234 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO H 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO O 233 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO O 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO O 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO O 234 " 0.028 5.00e-02 4.00e+02 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4121 2.80 - 3.33: 14026 3.33 - 3.85: 27142 3.85 - 4.38: 33011 4.38 - 4.90: 57882 Nonbonded interactions: 136182 Sorted by model distance: nonbonded pdb=" OE1 GLN H 144 " pdb=" OG1 THR H 241 " model vdw 2.277 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: 0.04 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.020 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 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 : 9.406 108.156 6396 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00220 (17271) covalent geometry : angle 0.48228 (23463) SS BOND : bond 0.00171 ( 21) SS BOND : angle 0.55133 ( 42) hydrogen bonds : bond 0.21641 ( 572) hydrogen bonds : angle 7.24599 ( 1623) link_ALPHA1-3 : bond 0.00438 ( 6) link_ALPHA1-3 : angle 1.46813 ( 18) link_ALPHA1-6 : bond 0.00394 ( 3) link_ALPHA1-6 : angle 1.44379 ( 9) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 2.23550 ( 18) link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 5.41568 ( 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 : 0.465 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: 0.6277 time to fit residues: 347.5546 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 : 0.453 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.069237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.045542 restraints weight = 45570.797| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.52 r_work: 0.2552 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17313 Z= 0.274 Angle : 0.679 8.089 23568 Z= 0.342 Chirality : 0.047 0.187 2628 Planarity : 0.005 0.052 2967 Dihedral : 8.600 90.641 2775 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.36 % Allowed : 13.85 % 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 aren not related in a simple way. whole: 0.87 (0.18), residues: 2115 helix: 1.80 (0.38), residues: 156 sheet: 0.87 (0.17), residues: 918 loop : 0.22 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.014 0.002 TYR A 104 PHE 0.020 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 covalent geometry : bond 0.00627 (17271) covalent geometry : angle 0.66732 (23463) SS BOND : bond 0.00518 ( 21) SS BOND : angle 0.98277 ( 42) hydrogen bonds : bond 0.03728 ( 572) hydrogen bonds : angle 5.01135 ( 1623) link_ALPHA1-3 : bond 0.00488 ( 6) link_ALPHA1-3 : angle 2.08156 ( 18) link_ALPHA1-6 : bond 0.00312 ( 3) link_ALPHA1-6 : angle 2.18730 ( 9) link_BETA1-4 : bond 0.00260 ( 6) link_BETA1-4 : angle 3.54289 ( 18) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 1.49179 ( 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 393 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 351 time to evaluate : 0.556 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 75 ASP cc_start: 0.8455 (t0) cc_final: 0.7933 (t0) REVERT: F 82 TYR cc_start: 0.9074 (m-80) cc_final: 0.8872 (m-80) REVERT: F 92 ASP cc_start: 0.9248 (m-30) cc_final: 0.8732 (m-30) REVERT: F 103 ARG cc_start: 0.9003 (mtp-110) cc_final: 0.8229 (ttp-110) REVERT: G 17 ARG cc_start: 0.9130 (mtp-110) cc_final: 0.8568 (ttp80) REVERT: G 85 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8145 (mm-30) REVERT: G 94 ASP cc_start: 0.8349 (t0) cc_final: 0.8129 (t70) REVERT: H 40 ARG cc_start: 0.8801 (mmm160) cc_final: 0.8582 (mmm-85) REVERT: H 46 GLU cc_start: 0.8333 (mp0) cc_final: 0.7940 (mp0) REVERT: H 59 ASP cc_start: 0.8720 (t0) cc_final: 0.8312 (t0) REVERT: H 73 ASP cc_start: 0.8607 (t0) cc_final: 0.8379 (t0) REVERT: H 220 ASP cc_start: 0.9080 (m-30) cc_final: 0.8829 (m-30) REVERT: A 105 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 85 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 40 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8441 (mmm160) REVERT: C 46 GLU cc_start: 0.8431 (mp0) cc_final: 0.8078 (mp0) REVERT: C 220 ASP cc_start: 0.9207 (m-30) cc_final: 0.8828 (m-30) REVERT: C 221 MET cc_start: 0.6248 (mmt) cc_final: 0.5572 (mmt) REVERT: K 46 GLU cc_start: 0.8627 (tt0) cc_final: 0.8135 (tt0) REVERT: K 103 ARG cc_start: 0.9066 (mtp-110) cc_final: 0.8537 (mtp-110) REVERT: K 105 ASN cc_start: 0.8587 (t0) cc_final: 0.8119 (p0) REVERT: K 107 ASP cc_start: 0.8892 (m-30) cc_final: 0.7917 (m-30) REVERT: L 94 ASP cc_start: 0.8021 (t0) cc_final: 0.7773 (t70) REVERT: O 40 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8519 (mmm160) REVERT: O 46 GLU cc_start: 0.8452 (mp0) cc_final: 0.7973 (mp0) REVERT: O 220 ASP cc_start: 0.9105 (m-30) cc_final: 0.8876 (m-30) REVERT: I 100 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8702 (mt-10) REVERT: I 112 GLU cc_start: 0.8043 (mp0) cc_final: 0.7841 (mp0) REVERT: I 228 ASN cc_start: 0.8550 (p0) cc_final: 0.8309 (p0) REVERT: I 231 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7652 (mt-10) REVERT: J 522 ASP cc_start: 0.8824 (t0) cc_final: 0.8603 (t0) REVERT: J 523 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: J 595 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8666 (tt0) REVERT: D 56 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8740 (mmmt) REVERT: D 112 GLU cc_start: 0.8034 (mp0) cc_final: 0.7793 (mp0) REVERT: D 228 ASN cc_start: 0.8224 (p0) cc_final: 0.7996 (p0) REVERT: E 523 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6735 (pt0) REVERT: M 112 GLU cc_start: 0.8190 (mp0) cc_final: 0.7916 (mp0) REVERT: M 136 ARG cc_start: 0.8488 (tpt90) cc_final: 0.7084 (tpm170) REVERT: M 178 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9050 (mt-10) REVERT: M 231 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7503 (mt-10) REVERT: N 540 GLU cc_start: 0.9133 (mp0) cc_final: 0.8929 (pm20) REVERT: N 595 GLN cc_start: 0.8982 (tp40) cc_final: 0.8570 (tt0) outliers start: 42 outliers final: 19 residues processed: 369 average time/residue: 0.6577 time to fit residues: 264.5924 Evaluate side-chains 343 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 A residue 105 ASN Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 90 THR 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 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: 0.8980 chunk 177 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 105 ASN A 31 ASN I 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.046825 restraints weight = 45815.836| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.51 r_work: 0.2583 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17313 Z= 0.128 Angle : 0.607 8.372 23568 Z= 0.304 Chirality : 0.043 0.170 2628 Planarity : 0.004 0.055 2967 Dihedral : 7.886 72.137 2763 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.75 % Allowed : 14.58 % Favored : 83.67 % 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 aren not related in a simple way. whole: 0.89 (0.18), residues: 2115 helix: 2.33 (0.39), residues: 156 sheet: 0.90 (0.17), residues: 924 loop : 0.11 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 587 TYR 0.014 0.001 TYR A 104 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 covalent geometry : bond 0.00284 (17271) covalent geometry : angle 0.59779 (23463) SS BOND : bond 0.00293 ( 21) SS BOND : angle 0.68551 ( 42) hydrogen bonds : bond 0.03050 ( 572) hydrogen bonds : angle 4.51035 ( 1623) link_ALPHA1-3 : bond 0.00677 ( 6) link_ALPHA1-3 : angle 1.45581 ( 18) link_ALPHA1-6 : bond 0.00156 ( 3) link_ALPHA1-6 : angle 1.94567 ( 9) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 2.90874 ( 18) link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 1.59741 ( 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 393 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 362 time to evaluate : 0.651 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: F 43 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8893 (mmmm) REVERT: F 46 GLU cc_start: 0.8303 (tt0) cc_final: 0.7994 (tt0) REVERT: F 75 ASP cc_start: 0.8507 (t0) cc_final: 0.7974 (t0) REVERT: F 82 TYR cc_start: 0.9098 (m-80) cc_final: 0.8865 (m-80) REVERT: F 103 ARG cc_start: 0.9043 (mtp-110) cc_final: 0.8585 (ttp80) REVERT: F 105 ASN cc_start: 0.8941 (m110) cc_final: 0.8622 (m-40) REVERT: G 85 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8172 (mm-30) REVERT: G 98 ARG cc_start: 0.8925 (mpp80) cc_final: 0.8703 (mpp80) REVERT: H 46 GLU cc_start: 0.8337 (mp0) cc_final: 0.7916 (mp0) REVERT: H 59 ASP cc_start: 0.8703 (t0) cc_final: 0.8301 (t0) REVERT: H 220 ASP cc_start: 0.9170 (m-30) cc_final: 0.8783 (m-30) REVERT: A 43 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8941 (mmmm) REVERT: A 105 ASN cc_start: 0.8666 (t0) cc_final: 0.8408 (p0) REVERT: B 85 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 109 LEU cc_start: 0.8809 (tp) cc_final: 0.8471 (tm) REVERT: C 40 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8433 (mmm160) REVERT: C 46 GLU cc_start: 0.8467 (mp0) cc_final: 0.8086 (mp0) REVERT: C 220 ASP cc_start: 0.9260 (m-30) cc_final: 0.8815 (m-30) REVERT: C 221 MET cc_start: 0.6247 (mmt) cc_final: 0.5483 (mmt) REVERT: K 43 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8818 (mmmm) REVERT: K 46 GLU cc_start: 0.8615 (tt0) cc_final: 0.8138 (tt0) REVERT: K 92 ASP cc_start: 0.9156 (m-30) cc_final: 0.8624 (m-30) REVERT: K 103 ARG cc_start: 0.9114 (mtp-110) cc_final: 0.8531 (ptm160) REVERT: K 107 ASP cc_start: 0.8915 (m-30) cc_final: 0.8454 (m-30) REVERT: L 85 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8498 (mm-30) REVERT: L 98 ARG cc_start: 0.8906 (mpp80) cc_final: 0.8507 (mmp80) REVERT: O 40 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8515 (mmm160) REVERT: O 46 GLU cc_start: 0.8426 (mp0) cc_final: 0.7945 (mp0) REVERT: O 220 ASP cc_start: 0.9221 (m-30) cc_final: 0.8847 (m-30) REVERT: I 100 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 112 GLU cc_start: 0.8054 (mp0) cc_final: 0.7767 (mp0) REVERT: J 522 ASP cc_start: 0.8871 (t0) cc_final: 0.8653 (t0) REVERT: J 523 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: J 544 THR cc_start: 0.9377 (m) cc_final: 0.9089 (p) REVERT: J 595 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8635 (tt0) REVERT: D 112 GLU cc_start: 0.8084 (mp0) cc_final: 0.7801 (mp0) REVERT: D 228 ASN cc_start: 0.8351 (p0) cc_final: 0.8147 (p0) REVERT: E 523 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: M 100 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8606 (pt0) REVERT: M 106 GLU cc_start: 0.8801 (tp30) cc_final: 0.8505 (tp30) REVERT: M 112 GLU cc_start: 0.8225 (mp0) cc_final: 0.7908 (mp0) REVERT: M 136 ARG cc_start: 0.8445 (tpt90) cc_final: 0.7299 (tpm170) REVERT: M 231 GLU cc_start: 0.7852 (mt-10) cc_final: 0.6981 (mt-10) REVERT: N 523 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6099 (pm20) REVERT: N 540 GLU cc_start: 0.9133 (mp0) cc_final: 0.8915 (pm20) outliers start: 31 outliers final: 13 residues processed: 376 average time/residue: 0.6604 time to fit residues: 270.8531 Evaluate side-chains 346 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 330 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 K residue 55 THR 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 M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 47 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 186 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN A 31 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.043264 restraints weight = 46314.900| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.54 r_work: 0.2488 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17313 Z= 0.309 Angle : 0.689 7.864 23568 Z= 0.347 Chirality : 0.046 0.173 2628 Planarity : 0.005 0.063 2967 Dihedral : 8.317 75.995 2763 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.36 % Allowed : 15.09 % Favored : 82.55 % 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 aren not related in a simple way. whole: 0.54 (0.18), residues: 2115 helix: 2.31 (0.41), residues: 156 sheet: 0.68 (0.17), residues: 915 loop : -0.17 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 587 TYR 0.025 0.002 TYR G 51 PHE 0.016 0.001 PHE K 97 TRP 0.015 0.002 TRP F 47 HIS 0.009 0.002 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00708 (17271) covalent geometry : angle 0.67662 (23463) SS BOND : bond 0.00520 ( 21) SS BOND : angle 1.11304 ( 42) hydrogen bonds : bond 0.03499 ( 572) hydrogen bonds : angle 4.58660 ( 1623) link_ALPHA1-3 : bond 0.00288 ( 6) link_ALPHA1-3 : angle 1.69618 ( 18) link_ALPHA1-6 : bond 0.00437 ( 3) link_ALPHA1-6 : angle 2.17116 ( 9) link_BETA1-4 : bond 0.00077 ( 6) link_BETA1-4 : angle 3.59179 ( 18) link_NAG-ASN : bond 0.00413 ( 6) link_NAG-ASN : angle 2.04921 ( 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 373 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8442 (tt0) cc_final: 0.8123 (tt0) REVERT: F 75 ASP cc_start: 0.8603 (t0) cc_final: 0.7947 (t0) REVERT: F 82 TYR cc_start: 0.9139 (m-80) cc_final: 0.8912 (m-80) REVERT: F 92 ASP cc_start: 0.9265 (m-30) cc_final: 0.8902 (m-30) REVERT: F 103 ARG cc_start: 0.8959 (mtp-110) cc_final: 0.8324 (ttp80) REVERT: F 105 ASN cc_start: 0.8979 (m110) cc_final: 0.8510 (m-40) REVERT: G 85 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8133 (mm-30) REVERT: H 46 GLU cc_start: 0.8443 (mp0) cc_final: 0.8103 (mp0) REVERT: H 59 ASP cc_start: 0.8789 (t0) cc_final: 0.8279 (t0) REVERT: H 220 ASP cc_start: 0.9177 (m-30) cc_final: 0.8812 (m-30) REVERT: A 75 ASP cc_start: 0.8523 (t0) cc_final: 0.7526 (t0) REVERT: A 92 ASP cc_start: 0.9233 (m-30) cc_final: 0.8749 (m-30) REVERT: A 103 ARG cc_start: 0.9032 (mtp-110) cc_final: 0.8710 (ttp80) REVERT: B 85 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 46 GLU cc_start: 0.8555 (mp0) cc_final: 0.8233 (mp0) REVERT: C 220 ASP cc_start: 0.9238 (m-30) cc_final: 0.8759 (m-30) REVERT: C 221 MET cc_start: 0.6363 (mmt) cc_final: 0.5551 (mmt) REVERT: K 46 GLU cc_start: 0.8614 (tt0) cc_final: 0.8154 (tt0) REVERT: K 75 ASP cc_start: 0.8575 (t0) cc_final: 0.7449 (t0) REVERT: K 89 LYS cc_start: 0.8551 (mmtp) cc_final: 0.8316 (mmtm) REVERT: K 92 ASP cc_start: 0.9246 (m-30) cc_final: 0.8771 (m-30) REVERT: K 103 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8804 (mtp-110) REVERT: L 85 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8490 (mm-30) REVERT: O 46 GLU cc_start: 0.8470 (mp0) cc_final: 0.8002 (mp0) REVERT: O 220 ASP cc_start: 0.9206 (m-30) cc_final: 0.8792 (m-30) REVERT: I 100 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8707 (mt-10) REVERT: I 112 GLU cc_start: 0.8122 (mp0) cc_final: 0.7809 (mp0) REVERT: I 156 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8850 (mm-30) REVERT: I 228 ASN cc_start: 0.8723 (p0) cc_final: 0.8447 (p0) REVERT: J 523 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: D 56 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8724 (mmmt) REVERT: D 112 GLU cc_start: 0.8105 (mp0) cc_final: 0.7762 (mp0) REVERT: E 523 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6799 (pt0) REVERT: M 106 GLU cc_start: 0.8885 (tp30) cc_final: 0.8641 (tp30) REVERT: M 112 GLU cc_start: 0.8252 (mp0) cc_final: 0.7914 (mp0) REVERT: M 231 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7618 (mt-10) REVERT: N 523 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6446 (pt0) REVERT: N 540 GLU cc_start: 0.9124 (mp0) cc_final: 0.8885 (pm20) REVERT: N 595 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8663 (tt0) outliers start: 42 outliers final: 19 residues processed: 351 average time/residue: 0.6839 time to fit residues: 261.5907 Evaluate side-chains 338 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 61 ASP Chi-restraints excluded: chain K residue 90 THR 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 I residue 156 GLU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain E residue 523 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN A 112 GLN B 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.044632 restraints weight = 45413.855| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.51 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: 0.8658 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17313 Z= 0.164 Angle : 0.649 8.543 23568 Z= 0.325 Chirality : 0.044 0.172 2628 Planarity : 0.005 0.062 2967 Dihedral : 7.801 69.574 2763 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.20 % Allowed : 16.78 % Favored : 81.02 % 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 aren not related in a simple way. whole: 0.57 (0.18), residues: 2115 helix: 2.48 (0.41), residues: 156 sheet: 0.77 (0.17), residues: 903 loop : -0.24 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 156 TYR 0.026 0.001 TYR G 51 PHE 0.011 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 covalent geometry : bond 0.00379 (17271) covalent geometry : angle 0.63863 (23463) SS BOND : bond 0.00342 ( 21) SS BOND : angle 0.77166 ( 42) hydrogen bonds : bond 0.02911 ( 572) hydrogen bonds : angle 4.35262 ( 1623) link_ALPHA1-3 : bond 0.00523 ( 6) link_ALPHA1-3 : angle 1.51639 ( 18) link_ALPHA1-6 : bond 0.00297 ( 3) link_ALPHA1-6 : angle 2.12236 ( 9) link_BETA1-4 : bond 0.00437 ( 6) link_BETA1-4 : angle 3.27243 ( 18) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.80441 ( 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 380 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 0.533 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: 0.8447 (tt0) cc_final: 0.8172 (tt0) REVERT: F 75 ASP cc_start: 0.8594 (t0) cc_final: 0.8057 (t0) REVERT: F 82 TYR cc_start: 0.9160 (m-80) cc_final: 0.8898 (m-80) REVERT: F 92 ASP cc_start: 0.9281 (m-30) cc_final: 0.8901 (m-30) REVERT: G 17 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8974 (mmm160) REVERT: G 68 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8996 (tttt) REVERT: G 85 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8139 (mm-30) REVERT: G 94 ASP cc_start: 0.8385 (t0) cc_final: 0.8163 (t0) REVERT: H 46 GLU cc_start: 0.8466 (mp0) cc_final: 0.8078 (mp0) REVERT: H 59 ASP cc_start: 0.8781 (t0) cc_final: 0.8249 (t0) REVERT: H 220 ASP cc_start: 0.9154 (m-30) cc_final: 0.8811 (m-30) REVERT: A 69 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8627 (mtm180) REVERT: A 75 ASP cc_start: 0.8409 (t0) cc_final: 0.7576 (t0) REVERT: A 92 ASP cc_start: 0.9227 (m-30) cc_final: 0.8798 (m-30) REVERT: A 103 ARG cc_start: 0.9069 (mtp-110) cc_final: 0.8618 (ttp80) REVERT: A 107 ASP cc_start: 0.7953 (p0) cc_final: 0.7575 (p0) REVERT: A 112 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: B 85 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 98 ARG cc_start: 0.8931 (mpp80) cc_final: 0.8534 (mmp80) REVERT: C 46 GLU cc_start: 0.8575 (mp0) cc_final: 0.8226 (mp0) REVERT: C 59 ASP cc_start: 0.8722 (t0) cc_final: 0.8481 (t0) REVERT: C 220 ASP cc_start: 0.9194 (m-30) cc_final: 0.8725 (m-30) REVERT: C 221 MET cc_start: 0.6345 (mmt) cc_final: 0.5519 (mmt) REVERT: K 43 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8798 (mmmm) REVERT: K 46 GLU cc_start: 0.8595 (tt0) cc_final: 0.8150 (tt0) REVERT: K 75 ASP cc_start: 0.8641 (t0) cc_final: 0.8172 (t0) REVERT: K 92 ASP cc_start: 0.9262 (m-30) cc_final: 0.8844 (m-30) REVERT: K 107 ASP cc_start: 0.8881 (m-30) cc_final: 0.8539 (p0) REVERT: L 85 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8495 (mm-30) REVERT: L 98 ARG cc_start: 0.9006 (mpp80) cc_final: 0.8803 (mpp80) REVERT: O 46 GLU cc_start: 0.8474 (mp0) cc_final: 0.7998 (mp0) REVERT: O 220 ASP cc_start: 0.9187 (m-30) cc_final: 0.8785 (m-30) REVERT: I 100 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8696 (mt-10) REVERT: I 112 GLU cc_start: 0.8130 (mp0) cc_final: 0.7835 (mp0) REVERT: I 228 ASN cc_start: 0.8823 (p0) cc_final: 0.8571 (p0) REVERT: J 523 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: J 544 THR cc_start: 0.9427 (m) cc_final: 0.9070 (p) REVERT: J 595 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8736 (tt0) REVERT: D 106 GLU cc_start: 0.8828 (tp30) cc_final: 0.8579 (tp30) REVERT: D 112 GLU cc_start: 0.8135 (mp0) cc_final: 0.7815 (mp0) REVERT: E 523 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: M 100 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8614 (pt0) REVERT: M 106 GLU cc_start: 0.8913 (tp30) cc_final: 0.8659 (tp30) REVERT: M 112 GLU cc_start: 0.8282 (mp0) cc_final: 0.7963 (mp0) REVERT: N 523 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: N 540 GLU cc_start: 0.9126 (mp0) cc_final: 0.8898 (pm20) REVERT: N 595 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8647 (tt0) outliers start: 39 outliers final: 26 residues processed: 362 average time/residue: 0.6574 time to fit residues: 259.5189 Evaluate side-chains 356 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain O residue 11 LEU 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 J residue 523 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 597 TRP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 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 597 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** 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 = 0.3293 r_free = 0.3293 target = 0.068583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.045335 restraints weight = 45698.682| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.49 r_work: 0.2545 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17313 Z= 0.151 Angle : 0.662 8.529 23568 Z= 0.330 Chirality : 0.044 0.186 2628 Planarity : 0.005 0.063 2967 Dihedral : 7.673 68.156 2763 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 17.51 % Favored : 80.24 % 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 aren not related in a simple way. whole: 0.57 (0.18), residues: 2115 helix: 2.57 (0.41), residues: 156 sheet: 0.75 (0.17), residues: 906 loop : -0.24 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 17 TYR 0.028 0.001 TYR G 51 PHE 0.015 0.001 PHE H 148 TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00354 (17271) covalent geometry : angle 0.65176 (23463) SS BOND : bond 0.00330 ( 21) SS BOND : angle 0.69888 ( 42) hydrogen bonds : bond 0.02776 ( 572) hydrogen bonds : angle 4.26872 ( 1623) link_ALPHA1-3 : bond 0.00579 ( 6) link_ALPHA1-3 : angle 1.56633 ( 18) link_ALPHA1-6 : bond 0.00253 ( 3) link_ALPHA1-6 : angle 2.08909 ( 9) link_BETA1-4 : bond 0.00488 ( 6) link_BETA1-4 : angle 3.25823 ( 18) link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 1.76238 ( 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 375 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 0.414 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: 0.8473 (tt0) cc_final: 0.8209 (tt0) REVERT: F 75 ASP cc_start: 0.8659 (t0) cc_final: 0.7614 (t0) REVERT: F 82 TYR cc_start: 0.9139 (m-80) cc_final: 0.8787 (m-80) REVERT: F 92 ASP cc_start: 0.9287 (m-30) cc_final: 0.8905 (m-30) REVERT: G 85 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8096 (mm-30) REVERT: G 98 ARG cc_start: 0.8855 (mpp80) cc_final: 0.8519 (mmp80) REVERT: H 46 GLU cc_start: 0.8454 (mp0) cc_final: 0.8082 (mp0) REVERT: H 59 ASP cc_start: 0.8793 (t0) cc_final: 0.8237 (t0) REVERT: H 220 ASP cc_start: 0.9142 (m-30) cc_final: 0.8819 (m-30) REVERT: A 43 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8804 (mmmm) REVERT: A 69 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8649 (mtm180) REVERT: A 75 ASP cc_start: 0.8433 (t0) cc_final: 0.7691 (t0) REVERT: A 92 ASP cc_start: 0.9221 (m-30) cc_final: 0.8790 (m-30) REVERT: A 103 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8633 (ttp80) REVERT: A 107 ASP cc_start: 0.8013 (p0) cc_final: 0.7563 (p0) REVERT: B 85 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 98 ARG cc_start: 0.8871 (mpp80) cc_final: 0.8606 (mmp80) REVERT: C 46 GLU cc_start: 0.8596 (mp0) cc_final: 0.8212 (mp0) REVERT: C 220 ASP cc_start: 0.9184 (m-30) cc_final: 0.8732 (m-30) REVERT: C 221 MET cc_start: 0.6329 (mmt) cc_final: 0.5498 (mmt) REVERT: K 43 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8766 (mmmm) REVERT: K 46 GLU cc_start: 0.8588 (tt0) cc_final: 0.8137 (tt0) REVERT: K 75 ASP cc_start: 0.8672 (t0) cc_final: 0.8188 (t0) REVERT: K 92 ASP cc_start: 0.9309 (m-30) cc_final: 0.8874 (m-30) REVERT: K 105 ASN cc_start: 0.8907 (m110) cc_final: 0.8566 (p0) REVERT: K 107 ASP cc_start: 0.8830 (m-30) cc_final: 0.8051 (p0) REVERT: L 81 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8517 (mm-40) REVERT: L 85 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8494 (mm-30) REVERT: L 98 ARG cc_start: 0.8881 (mpp80) cc_final: 0.8621 (mmp80) REVERT: O 46 GLU cc_start: 0.8483 (mp0) cc_final: 0.8002 (mp0) REVERT: O 220 ASP cc_start: 0.9188 (m-30) cc_final: 0.8806 (m-30) REVERT: I 100 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8641 (mt-10) REVERT: I 112 GLU cc_start: 0.8124 (mp0) cc_final: 0.7788 (mp0) REVERT: J 544 THR cc_start: 0.9426 (m) cc_final: 0.9082 (p) REVERT: J 595 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8691 (tt0) REVERT: D 56 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8742 (mmmt) REVERT: D 106 GLU cc_start: 0.8849 (tp30) cc_final: 0.8586 (tp30) REVERT: D 112 GLU cc_start: 0.8104 (mp0) cc_final: 0.7770 (mp0) REVERT: E 523 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: M 100 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8681 (pt0) REVERT: M 106 GLU cc_start: 0.8838 (tp30) cc_final: 0.8579 (tp30) REVERT: M 112 GLU cc_start: 0.8257 (mp0) cc_final: 0.7919 (mp0) REVERT: N 540 GLU cc_start: 0.9132 (mp0) cc_final: 0.8914 (pm20) REVERT: N 595 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8653 (tt0) outliers start: 40 outliers final: 26 residues processed: 358 average time/residue: 0.6312 time to fit residues: 246.8438 Evaluate side-chains 352 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 ARG 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 76 ASP Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain O residue 11 LEU 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 O residue 166 ASP Chi-restraints excluded: chain I residue 55 ASP 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 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 576 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3261 r_free = 0.3261 target = 0.067188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.043456 restraints weight = 45647.597| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.51 r_work: 0.2501 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17313 Z= 0.270 Angle : 0.712 9.066 23568 Z= 0.359 Chirality : 0.045 0.173 2628 Planarity : 0.005 0.065 2967 Dihedral : 7.974 71.434 2763 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.25 % Allowed : 17.96 % 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 aren not related in a simple way. whole: 0.42 (0.18), residues: 2115 helix: 2.51 (0.42), residues: 156 sheet: 0.62 (0.17), residues: 912 loop : -0.32 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 17 TYR 0.028 0.002 TYR G 51 PHE 0.015 0.001 PHE A 97 TRP 0.015 0.001 TRP F 47 HIS 0.008 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00623 (17271) covalent geometry : angle 0.70047 (23463) SS BOND : bond 0.00463 ( 21) SS BOND : angle 0.94740 ( 42) hydrogen bonds : bond 0.03137 ( 572) hydrogen bonds : angle 4.41383 ( 1623) link_ALPHA1-3 : bond 0.00322 ( 6) link_ALPHA1-3 : angle 1.64654 ( 18) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 2.17617 ( 9) link_BETA1-4 : bond 0.00166 ( 6) link_BETA1-4 : angle 3.60050 ( 18) link_NAG-ASN : bond 0.00075 ( 6) link_NAG-ASN : angle 1.85799 ( 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 369 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.447 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: 0.8509 (tt0) cc_final: 0.8194 (tt0) REVERT: F 54 LYS cc_start: 0.9522 (tppp) cc_final: 0.9318 (tppt) REVERT: F 75 ASP cc_start: 0.8815 (t0) cc_final: 0.8103 (t0) REVERT: F 78 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9224 (mtmp) REVERT: F 82 TYR cc_start: 0.8979 (m-80) cc_final: 0.8683 (m-80) REVERT: F 89 LYS cc_start: 0.8252 (mmtp) cc_final: 0.8051 (mmtt) REVERT: F 92 ASP cc_start: 0.9326 (m-30) cc_final: 0.8997 (m-30) REVERT: G 68 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8861 (tttp) REVERT: G 85 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8163 (mm-30) REVERT: H 46 GLU cc_start: 0.8504 (mp0) cc_final: 0.8127 (mp0) REVERT: H 59 ASP cc_start: 0.8831 (t0) cc_final: 0.8346 (t0) REVERT: H 220 ASP cc_start: 0.9135 (m-30) cc_final: 0.8828 (m-30) REVERT: A 43 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8734 (mmmm) REVERT: A 54 LYS cc_start: 0.9479 (tppt) cc_final: 0.9190 (mppt) REVERT: A 75 ASP cc_start: 0.8454 (t0) cc_final: 0.7529 (t0) REVERT: A 89 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7931 (mmtt) REVERT: A 92 ASP cc_start: 0.9230 (m-30) cc_final: 0.8761 (m-30) REVERT: A 103 ARG cc_start: 0.9067 (mtp-110) cc_final: 0.8699 (ttp80) REVERT: A 107 ASP cc_start: 0.8028 (p0) cc_final: 0.7808 (p0) REVERT: B 85 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8506 (mm-30) REVERT: C 46 GLU cc_start: 0.8645 (mp0) cc_final: 0.8285 (mp0) REVERT: C 59 ASP cc_start: 0.8732 (t0) cc_final: 0.8491 (t0) REVERT: C 220 ASP cc_start: 0.9168 (m-30) cc_final: 0.8711 (m-30) REVERT: C 221 MET cc_start: 0.6367 (mmt) cc_final: 0.5556 (mmt) REVERT: K 46 GLU cc_start: 0.8592 (tt0) cc_final: 0.8160 (tt0) REVERT: K 75 ASP cc_start: 0.8899 (t0) cc_final: 0.8270 (t0) REVERT: K 89 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7831 (mmtt) REVERT: K 92 ASP cc_start: 0.9296 (m-30) cc_final: 0.8905 (m-30) REVERT: L 85 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8502 (mm-30) REVERT: O 46 GLU cc_start: 0.8535 (mp0) cc_final: 0.8060 (mp0) REVERT: O 156 ARG cc_start: 0.9428 (mtp-110) cc_final: 0.9132 (ttm110) REVERT: O 220 ASP cc_start: 0.9159 (m-30) cc_final: 0.8808 (m-30) REVERT: I 100 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8690 (mt-10) REVERT: I 106 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8205 (tp30) REVERT: I 112 GLU cc_start: 0.8156 (mp0) cc_final: 0.7811 (mp0) REVERT: I 136 ARG cc_start: 0.8681 (tpm-80) cc_final: 0.8412 (tpm-80) REVERT: J 595 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8822 (tt0) REVERT: D 56 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8727 (mmmt) REVERT: D 106 GLU cc_start: 0.8883 (tp30) cc_final: 0.8643 (tp30) REVERT: D 112 GLU cc_start: 0.8143 (mp0) cc_final: 0.7798 (mp0) REVERT: E 523 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: M 106 GLU cc_start: 0.8871 (tp30) cc_final: 0.8621 (tp30) REVERT: M 112 GLU cc_start: 0.8253 (mp0) cc_final: 0.7880 (mp0) REVERT: N 523 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: N 540 GLU cc_start: 0.9130 (mp0) cc_final: 0.8893 (pm20) outliers start: 40 outliers final: 28 residues processed: 350 average time/residue: 0.6538 time to fit residues: 248.9251 Evaluate side-chains 354 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR 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 F residue 107 ASP Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR 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 61 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 597 TRP 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 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 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: 4.9990 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 161 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN ** 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 = 0.3290 r_free = 0.3290 target = 0.068557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.045006 restraints weight = 45658.577| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 3.53 r_work: 0.2548 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17313 Z= 0.131 Angle : 0.690 9.791 23568 Z= 0.345 Chirality : 0.044 0.178 2628 Planarity : 0.005 0.062 2967 Dihedral : 7.521 65.313 2763 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.97 % Allowed : 19.43 % Favored : 78.60 % 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 aren not related in a simple way. whole: 0.55 (0.18), residues: 2115 helix: 2.63 (0.42), residues: 156 sheet: 0.81 (0.17), residues: 870 loop : -0.30 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 156 TYR 0.030 0.001 TYR G 51 PHE 0.015 0.001 PHE H 148 TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS O 229 Details of bonding type rmsd covalent geometry : bond 0.00309 (17271) covalent geometry : angle 0.68110 (23463) SS BOND : bond 0.00293 ( 21) SS BOND : angle 0.63991 ( 42) hydrogen bonds : bond 0.02644 ( 572) hydrogen bonds : angle 4.23633 ( 1623) link_ALPHA1-3 : bond 0.00632 ( 6) link_ALPHA1-3 : angle 1.54280 ( 18) link_ALPHA1-6 : bond 0.00181 ( 3) link_ALPHA1-6 : angle 2.04897 ( 9) link_BETA1-4 : bond 0.00577 ( 6) link_BETA1-4 : angle 3.22834 ( 18) link_NAG-ASN : bond 0.00340 ( 6) link_NAG-ASN : angle 1.73452 ( 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 369 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 0.653 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: 0.8476 (tt0) cc_final: 0.8163 (tt0) REVERT: F 75 ASP cc_start: 0.8858 (t0) cc_final: 0.8098 (t0) REVERT: F 78 LYS cc_start: 0.9524 (mtmm) cc_final: 0.9228 (mtmm) REVERT: F 82 TYR cc_start: 0.9024 (m-80) cc_final: 0.8764 (m-80) REVERT: F 89 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7814 (mmtt) REVERT: F 92 ASP cc_start: 0.9311 (m-30) cc_final: 0.8923 (m-30) REVERT: F 105 ASN cc_start: 0.9068 (m110) cc_final: 0.8692 (p0) REVERT: G 85 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8080 (mm-30) REVERT: G 98 ARG cc_start: 0.8835 (mpp80) cc_final: 0.8505 (mmp80) REVERT: H 46 GLU cc_start: 0.8522 (mp0) cc_final: 0.8124 (mp0) REVERT: H 59 ASP cc_start: 0.8809 (t0) cc_final: 0.8319 (t0) REVERT: H 220 ASP cc_start: 0.9123 (m-30) cc_final: 0.8837 (m-30) REVERT: A 43 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8696 (mmmm) REVERT: A 54 LYS cc_start: 0.9479 (tppt) cc_final: 0.9190 (mppt) REVERT: A 75 ASP cc_start: 0.8354 (t0) cc_final: 0.7490 (t0) REVERT: A 88 LEU cc_start: 0.9011 (mm) cc_final: 0.8786 (mm) REVERT: A 89 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8046 (mmtt) REVERT: A 92 ASP cc_start: 0.9175 (m-30) cc_final: 0.8721 (m-30) REVERT: A 103 ARG cc_start: 0.9105 (mtp-110) cc_final: 0.8631 (ttp80) REVERT: A 107 ASP cc_start: 0.7973 (p0) cc_final: 0.7433 (p0) REVERT: B 81 GLN cc_start: 0.8849 (mm110) cc_final: 0.8648 (mp10) REVERT: B 85 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8483 (mm-30) REVERT: B 98 ARG cc_start: 0.8849 (mpp80) cc_final: 0.8460 (mmp80) REVERT: C 46 GLU cc_start: 0.8652 (mp0) cc_final: 0.8279 (mp0) REVERT: C 59 ASP cc_start: 0.8716 (t0) cc_final: 0.8454 (t0) REVERT: C 220 ASP cc_start: 0.9183 (m-30) cc_final: 0.8780 (m-30) REVERT: C 221 MET cc_start: 0.6322 (mmt) cc_final: 0.5537 (mmt) REVERT: K 43 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8686 (mmmm) REVERT: K 46 GLU cc_start: 0.8571 (tt0) cc_final: 0.8146 (tt0) REVERT: K 75 ASP cc_start: 0.8826 (t0) cc_final: 0.8146 (t0) REVERT: K 92 ASP cc_start: 0.9326 (m-30) cc_final: 0.8896 (m-30) REVERT: K 105 ASN cc_start: 0.8931 (m110) cc_final: 0.8542 (p0) REVERT: K 107 ASP cc_start: 0.8726 (m-30) cc_final: 0.7673 (p0) REVERT: L 85 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8525 (mm-30) REVERT: O 46 GLU cc_start: 0.8474 (mp0) cc_final: 0.7995 (mp0) REVERT: O 220 ASP cc_start: 0.9172 (m-30) cc_final: 0.8827 (m-30) REVERT: I 100 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8629 (mt-10) REVERT: I 112 GLU cc_start: 0.8147 (mp0) cc_final: 0.7810 (mp0) REVERT: J 544 THR cc_start: 0.9429 (m) cc_final: 0.9066 (p) REVERT: J 595 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8721 (tt0) REVERT: D 56 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8721 (mmmt) REVERT: D 100 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8827 (pt0) REVERT: D 106 GLU cc_start: 0.8885 (tp30) cc_final: 0.8634 (tp30) REVERT: D 112 GLU cc_start: 0.8122 (mp0) cc_final: 0.7778 (mp0) REVERT: D 156 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8999 (mm-30) REVERT: M 100 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8705 (pt0) REVERT: M 106 GLU cc_start: 0.8849 (tp30) cc_final: 0.8591 (tp30) REVERT: M 112 GLU cc_start: 0.8256 (mp0) cc_final: 0.7910 (mp0) REVERT: N 540 GLU cc_start: 0.9138 (mp0) cc_final: 0.8933 (pm20) REVERT: N 595 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8660 (tt0) outliers start: 35 outliers final: 24 residues processed: 355 average time/residue: 0.6589 time to fit residues: 255.9322 Evaluate side-chains 347 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 322 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 107 ASP 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 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 O residue 11 LEU 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 576 THR Chi-restraints excluded: chain J residue 597 TRP 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 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 576 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: 0.8980 chunk 201 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.067617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.043885 restraints weight = 45863.745| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.53 r_work: 0.2515 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17313 Z= 0.224 Angle : 0.737 11.746 23568 Z= 0.368 Chirality : 0.045 0.171 2628 Planarity : 0.005 0.064 2967 Dihedral : 7.744 68.201 2763 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.52 % Allowed : 19.93 % Favored : 78.55 % 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 aren not related in a simple way. whole: 0.51 (0.18), residues: 2115 helix: 2.66 (0.42), residues: 156 sheet: 0.77 (0.18), residues: 864 loop : -0.33 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 156 TYR 0.033 0.001 TYR G 51 PHE 0.013 0.001 PHE A 97 TRP 0.014 0.001 TRP F 47 HIS 0.007 0.001 HIS O 229 Details of bonding type rmsd covalent geometry : bond 0.00523 (17271) covalent geometry : angle 0.72689 (23463) SS BOND : bond 0.00411 ( 21) SS BOND : angle 0.86717 ( 42) hydrogen bonds : bond 0.02937 ( 572) hydrogen bonds : angle 4.29175 ( 1623) link_ALPHA1-3 : bond 0.00383 ( 6) link_ALPHA1-3 : angle 1.60056 ( 18) link_ALPHA1-6 : bond 0.00427 ( 3) link_ALPHA1-6 : angle 2.12432 ( 9) link_BETA1-4 : bond 0.00302 ( 6) link_BETA1-4 : angle 3.50438 ( 18) link_NAG-ASN : bond 0.00146 ( 6) link_NAG-ASN : angle 1.79999 ( 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 354 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 0.481 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: 0.8496 (tt0) cc_final: 0.8137 (tt0) REVERT: F 54 LYS cc_start: 0.9493 (tppt) cc_final: 0.9278 (mppt) REVERT: F 75 ASP cc_start: 0.8869 (t0) cc_final: 0.8398 (t0) REVERT: F 89 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7871 (mmtt) REVERT: F 92 ASP cc_start: 0.9297 (m-30) cc_final: 0.8923 (m-30) REVERT: F 105 ASN cc_start: 0.9058 (m110) cc_final: 0.8667 (p0) REVERT: G 85 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8109 (mm-30) REVERT: G 98 ARG cc_start: 0.8925 (mpp80) cc_final: 0.8547 (mmp80) REVERT: H 46 GLU cc_start: 0.8540 (mp0) cc_final: 0.8088 (mp0) REVERT: H 59 ASP cc_start: 0.8840 (t0) cc_final: 0.8345 (t0) REVERT: H 220 ASP cc_start: 0.9140 (m-30) cc_final: 0.8850 (m-30) REVERT: A 43 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8773 (mmmm) REVERT: A 75 ASP cc_start: 0.8439 (t0) cc_final: 0.7451 (t0) REVERT: A 78 LYS cc_start: 0.9538 (ptpp) cc_final: 0.9261 (ptpp) REVERT: A 89 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8005 (mptt) REVERT: A 92 ASP cc_start: 0.9171 (m-30) cc_final: 0.8721 (m-30) REVERT: A 103 ARG cc_start: 0.9104 (mtp-110) cc_final: 0.8731 (ttp80) REVERT: A 107 ASP cc_start: 0.8061 (p0) cc_final: 0.7824 (p0) REVERT: B 85 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 98 ARG cc_start: 0.8956 (mpp80) cc_final: 0.8568 (mmp80) REVERT: C 46 GLU cc_start: 0.8671 (mp0) cc_final: 0.8302 (mp0) REVERT: C 59 ASP cc_start: 0.8771 (t0) cc_final: 0.8512 (t0) REVERT: C 220 ASP cc_start: 0.9180 (m-30) cc_final: 0.8795 (m-30) REVERT: C 221 MET cc_start: 0.6334 (mmt) cc_final: 0.5541 (mmt) REVERT: K 43 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8746 (mmmm) REVERT: K 46 GLU cc_start: 0.8589 (tt0) cc_final: 0.8165 (tt0) REVERT: K 75 ASP cc_start: 0.8777 (t0) cc_final: 0.8146 (t0) REVERT: K 89 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7875 (mmtt) REVERT: K 92 ASP cc_start: 0.9311 (m-30) cc_final: 0.8898 (m-30) REVERT: K 107 ASP cc_start: 0.8695 (m-30) cc_final: 0.8158 (p0) REVERT: L 85 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8590 (mm-30) REVERT: L 111 VAL cc_start: 0.8469 (t) cc_final: 0.8255 (p) REVERT: O 46 GLU cc_start: 0.8516 (mp0) cc_final: 0.8036 (mp0) REVERT: O 156 ARG cc_start: 0.9424 (mtp-110) cc_final: 0.9116 (ttm110) REVERT: O 220 ASP cc_start: 0.9202 (m-30) cc_final: 0.8879 (m-30) REVERT: I 100 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8690 (mt-10) REVERT: I 112 GLU cc_start: 0.8146 (mp0) cc_final: 0.7787 (mp0) REVERT: I 136 ARG cc_start: 0.8672 (tpm-80) cc_final: 0.8375 (tpm-80) REVERT: J 544 THR cc_start: 0.9450 (m) cc_final: 0.9053 (p) REVERT: J 595 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8814 (tt0) REVERT: D 56 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8713 (mmmt) REVERT: D 106 GLU cc_start: 0.8878 (tp30) cc_final: 0.8634 (tp30) REVERT: D 112 GLU cc_start: 0.8135 (mp0) cc_final: 0.7762 (mp0) REVERT: M 100 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8782 (pt0) REVERT: M 106 GLU cc_start: 0.8849 (tp30) cc_final: 0.8599 (tp30) REVERT: M 112 GLU cc_start: 0.8228 (mp0) cc_final: 0.7834 (mp0) REVERT: N 540 GLU cc_start: 0.9132 (mp0) cc_final: 0.8896 (pm20) REVERT: N 595 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8690 (tt0) outliers start: 27 outliers final: 25 residues processed: 344 average time/residue: 0.6604 time to fit residues: 248.0430 Evaluate side-chains 348 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR 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 61 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain O residue 11 LEU 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 576 THR Chi-restraints excluded: chain J residue 597 TRP 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 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: 9.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3255 r_free = 0.3255 target = 0.066856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.043153 restraints weight = 46219.162| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.52 r_work: 0.2496 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 17313 Z= 0.308 Angle : 0.774 10.328 23568 Z= 0.389 Chirality : 0.046 0.208 2628 Planarity : 0.006 0.065 2967 Dihedral : 7.964 70.758 2763 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 20.66 % Favored : 78.04 % 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 aren not related in a simple way. whole: 0.36 (0.18), residues: 2115 helix: 2.65 (0.42), residues: 156 sheet: 0.58 (0.17), residues: 897 loop : -0.39 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 587 TYR 0.033 0.002 TYR G 51 PHE 0.017 0.001 PHE H 148 TRP 0.015 0.001 TRP F 47 HIS 0.008 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00715 (17271) covalent geometry : angle 0.76363 (23463) SS BOND : bond 0.00474 ( 21) SS BOND : angle 1.02536 ( 42) hydrogen bonds : bond 0.03145 ( 572) hydrogen bonds : angle 4.38562 ( 1623) link_ALPHA1-3 : bond 0.00294 ( 6) link_ALPHA1-3 : angle 1.60794 ( 18) link_ALPHA1-6 : bond 0.00640 ( 3) link_ALPHA1-6 : angle 2.19284 ( 9) link_BETA1-4 : bond 0.00098 ( 6) link_BETA1-4 : angle 3.71993 ( 18) link_NAG-ASN : bond 0.00074 ( 6) link_NAG-ASN : angle 1.84592 ( 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 344 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 0.553 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: F 54 LYS cc_start: 0.9505 (tppt) cc_final: 0.9279 (mppt) REVERT: F 75 ASP cc_start: 0.8835 (t0) cc_final: 0.8424 (t0) REVERT: F 76 ASP cc_start: 0.8605 (m-30) cc_final: 0.8396 (m-30) REVERT: F 89 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7942 (mmtt) REVERT: F 92 ASP cc_start: 0.9286 (m-30) cc_final: 0.8939 (m-30) REVERT: G 85 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8087 (mm-30) REVERT: H 46 GLU cc_start: 0.8547 (mp0) cc_final: 0.8148 (mp0) REVERT: H 59 ASP cc_start: 0.8876 (t0) cc_final: 0.8375 (t0) REVERT: H 220 ASP cc_start: 0.9137 (m-30) cc_final: 0.8881 (m-30) REVERT: A 43 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8804 (mmmm) REVERT: A 54 LYS cc_start: 0.9467 (tppt) cc_final: 0.9214 (mppt) REVERT: A 75 ASP cc_start: 0.8457 (t0) cc_final: 0.7461 (t0) REVERT: A 78 LYS cc_start: 0.9561 (ptpp) cc_final: 0.9273 (ptpp) REVERT: A 89 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8027 (mmtt) REVERT: A 92 ASP cc_start: 0.9203 (m-30) cc_final: 0.8790 (m-30) REVERT: A 103 ARG cc_start: 0.9082 (mtp-110) cc_final: 0.8703 (ttp80) REVERT: A 107 ASP cc_start: 0.8091 (p0) cc_final: 0.7834 (p0) REVERT: B 85 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8410 (mm-30) REVERT: B 98 ARG cc_start: 0.8992 (mpp80) cc_final: 0.8617 (mmp80) REVERT: C 46 GLU cc_start: 0.8686 (mp0) cc_final: 0.8227 (mp0) REVERT: C 59 ASP cc_start: 0.8788 (t0) cc_final: 0.8515 (t0) REVERT: C 220 ASP cc_start: 0.9168 (m-30) cc_final: 0.8792 (m-30) REVERT: C 221 MET cc_start: 0.6368 (mmt) cc_final: 0.5585 (mmt) REVERT: K 43 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8740 (mmmm) REVERT: K 46 GLU cc_start: 0.8591 (tt0) cc_final: 0.8163 (tt0) REVERT: K 75 ASP cc_start: 0.8768 (t0) cc_final: 0.8141 (t0) REVERT: K 89 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7905 (mmtt) REVERT: K 92 ASP cc_start: 0.9324 (m-30) cc_final: 0.8969 (m-30) REVERT: K 107 ASP cc_start: 0.8671 (m-30) cc_final: 0.8122 (p0) REVERT: L 17 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7784 (ttp80) REVERT: L 85 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8594 (mm-30) REVERT: L 111 VAL cc_start: 0.8456 (t) cc_final: 0.8245 (p) REVERT: O 46 GLU cc_start: 0.8535 (mp0) cc_final: 0.8056 (mp0) REVERT: O 156 ARG cc_start: 0.9432 (mtp-110) cc_final: 0.9123 (ttm110) REVERT: I 100 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8687 (mt-10) REVERT: I 112 GLU cc_start: 0.8176 (mp0) cc_final: 0.7815 (mp0) REVERT: I 136 ARG cc_start: 0.8679 (tpm-80) cc_final: 0.8375 (tpm-80) REVERT: D 56 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8712 (mmmt) REVERT: D 106 GLU cc_start: 0.8905 (tp30) cc_final: 0.8645 (tp30) REVERT: D 112 GLU cc_start: 0.8138 (mp0) cc_final: 0.7790 (mp0) REVERT: M 100 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8718 (pt0) REVERT: M 106 GLU cc_start: 0.8860 (tp30) cc_final: 0.8617 (tp30) REVERT: M 112 GLU cc_start: 0.8235 (mp0) cc_final: 0.7852 (mp0) REVERT: N 523 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: N 540 GLU cc_start: 0.9122 (mp0) cc_final: 0.8884 (pm20) REVERT: N 595 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8706 (tt0) outliers start: 23 outliers final: 23 residues processed: 335 average time/residue: 0.6698 time to fit residues: 244.7109 Evaluate side-chains 344 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 319 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 107 ASP 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 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 O residue 11 LEU 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 J residue 597 TRP 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 522 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3288 r_free = 0.3288 target = 0.068377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.044841 restraints weight = 45325.462| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.51 r_work: 0.2542 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17313 Z= 0.142 Angle : 0.743 10.778 23568 Z= 0.370 Chirality : 0.044 0.173 2628 Planarity : 0.005 0.064 2967 Dihedral : 7.496 64.322 2763 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.35 % Allowed : 20.55 % Favored : 78.10 % 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 aren not related in a simple way. whole: 0.50 (0.18), residues: 2115 helix: 2.71 (0.42), residues: 156 sheet: 0.80 (0.18), residues: 867 loop : -0.38 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 156 TYR 0.034 0.001 TYR G 51 PHE 0.008 0.001 PHE A 97 TRP 0.013 0.001 TRP F 47 HIS 0.005 0.001 HIS O 229 Details of bonding type rmsd covalent geometry : bond 0.00342 (17271) covalent geometry : angle 0.73429 (23463) SS BOND : bond 0.00303 ( 21) SS BOND : angle 0.65722 ( 42) hydrogen bonds : bond 0.02654 ( 572) hydrogen bonds : angle 4.21637 ( 1623) link_ALPHA1-3 : bond 0.00614 ( 6) link_ALPHA1-3 : angle 1.53211 ( 18) link_ALPHA1-6 : bond 0.00245 ( 3) link_ALPHA1-6 : angle 2.06355 ( 9) link_BETA1-4 : bond 0.00552 ( 6) link_BETA1-4 : angle 3.29624 ( 18) link_NAG-ASN : bond 0.00346 ( 6) link_NAG-ASN : angle 1.75085 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6612.53 seconds wall clock time: 113 minutes 0.54 seconds (6780.54 seconds total)