Starting phenix.real_space_refine on Sun Aug 24 17:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpm_27638/08_2025/8dpm_27638.map" } resolution = 3.0 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= -0.000 sd= 0.002 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 5526 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 69 5.16 5 C 10725 2.51 5 N 2886 2.21 5 O 3312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s 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: 16992 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "G" 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: "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: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "B" 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: "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: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "K" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "L" 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: 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: "N" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} 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: "F" 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: "A" 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: "K" 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: 3.69, per 1000 atoms: 0.22 Number of scatterers: 16992 At special positions: 0 Unit cell: (126, 127.05, 112.35, 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 69 16.00 O 3312 8.00 N 2886 7.00 C 10725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 135 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " 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 I 22 " - pdb=" SG CYS I 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " 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 D 22 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 135 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS K 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 511 " - pdb=" SG CYS L 556 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 161 " - pdb=" SG CYS M 226 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " 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 A 401 " - " ASN A 228 " " NAG F 401 " - " ASN F 228 " " NAG K 401 " - " ASN K 228 " " NAG P 1 " - " ASN G 563 " " NAG Q 1 " - " ASN B 563 " " NAG R 1 " - " ASN L 563 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 689.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 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: 15 helices and 45 sheets defined 7.7% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 552 through 576 removed outlier: 3.636A pdb=" N CYS G 556 " --> pdb=" O ASP G 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN G 567 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU J 85 " --> pdb=" O THR J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'B' and resid 552 through 576 removed outlier: 3.644A pdb=" N CYS B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.905A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'L' and resid 552 through 576 removed outlier: 3.642A pdb=" N CYS L 556 " --> pdb=" O ASP L 552 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN L 567 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA L 568 " --> pdb=" O GLU L 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 571 " --> pdb=" O GLN L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 597 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP O 84 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN F 69 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 96 " --> pdb=" O THR G 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'F' and resid 108 through 114 removed outlier: 6.816A pdb=" N CYS F 108 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 141 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN F 110 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY F 143 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU F 112 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 138 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR F 220 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 140 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA F 222 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER F 142 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.694A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA8, 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) Processing sheet with id=AA9, first strand: chain 'H' and resid 183 through 186 removed outlier: 6.682A pdb=" N TRP H 173 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 223 " --> pdb=" O GLN H 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.874A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 37 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 102 through 104 Processing sheet with id=AB4, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP J 87 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC1, first strand: chain 'A' and resid 108 through 114 removed outlier: 6.827A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.689A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.973A pdb=" N GLY C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.636A pdb=" N VAL C 157 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 186 removed outlier: 6.676A pdb=" N TRP C 173 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 223 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.860A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 37 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 87 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN K 69 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 96 " --> pdb=" O THR L 581 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 86 through 89 Processing sheet with id=AD6, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY K 143 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL K 138 " --> pdb=" O ILE K 218 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR K 220 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS K 140 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA K 222 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER K 142 " --> pdb=" O ALA K 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.697A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR M 107 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 142 through 144 removed outlier: 3.632A pdb=" N VAL M 157 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 183 through 186 removed outlier: 6.684A pdb=" N TRP M 173 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 223 " --> pdb=" O GLN M 176 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AE5, first strand: chain 'N' and resid 60 through 62 removed outlier: 6.867A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET N 34 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL N 37 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 102 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP O 87 " --> pdb=" O HIS O 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 18 through 23 556 hydrogen bonds defined for protein. 1410 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: 2.86 Time building geometry restraints manager: 1.98 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: 5454 1.34 - 1.46: 4069 1.46 - 1.58: 7775 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 17391 Sorted by residual: bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 MAN Q 4 " pdb=" C2 MAN Q 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 MAN P 6 " pdb=" C2 MAN P 6 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 MAN Q 6 " pdb=" C2 MAN Q 6 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 17386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 23051 1.30 - 2.61: 404 2.61 - 3.91: 101 3.91 - 5.21: 39 5.21 - 6.51: 18 Bond angle restraints: 23613 Sorted by residual: angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" N THR C 241 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.20e+00 angle pdb=" C GLN G 551 " pdb=" N ASP G 552 " pdb=" CA ASP G 552 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" C GLN L 551 " pdb=" N ASP L 552 " pdb=" CA ASP L 552 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.29e+00 angle pdb=" C GLN B 551 " pdb=" N ASP B 552 " pdb=" CA ASP B 552 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.16e+00 angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" O GLY C 240 " ideal model delta sigma weight residual 122.33 120.57 1.76 8.10e-01 1.52e+00 4.71e+00 ... (remaining 23608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10148 21.43 - 42.87: 213 42.87 - 64.30: 31 64.30 - 85.74: 27 85.74 - 107.17: 12 Dihedral angle restraints: 10431 sinusoidal: 4299 harmonic: 6132 Sorted by residual: dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.46 107.17 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.44 107.15 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.41 107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2372 0.072 - 0.144: 251 0.144 - 0.216: 2 0.216 - 0.288: 3 0.288 - 0.360: 6 Chirality restraints: 2634 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN L 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2631 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 234 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 233 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO M 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO M 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 234 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.94e+00 pdb=" N PRO H 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " -0.024 5.00e-02 4.00e+02 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2055 2.76 - 3.29: 16011 3.29 - 3.83: 28969 3.83 - 4.36: 35505 4.36 - 4.90: 62154 Nonbonded interactions: 144694 Sorted by model distance: nonbonded pdb=" OG SER F 65 " pdb=" OE1 GLU F 100 " model vdw 2.221 3.040 nonbonded pdb=" OG SER K 65 " pdb=" OE1 GLU K 100 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 65 " pdb=" OE1 GLU A 100 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 117 " pdb=" OG SER A 119 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR O 33 " pdb=" OD1 ASP O 99 " model vdw 2.271 3.040 ... (remaining 144689 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: 0.06 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 'M' } ncs_group { reference = chain 'I' selection = chain 'D' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'E' selection = chain 'O' } 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.039 17433 Z= 0.123 Angle : 0.580 25.680 23718 Z= 0.271 Chirality : 0.044 0.360 2634 Planarity : 0.003 0.043 3000 Dihedral : 10.748 107.173 6486 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.62 % Allowed : 5.04 % Favored : 94.34 % 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: 0.12 (0.18), residues: 2127 helix: 0.01 (0.45), residues: 156 sheet: 0.19 (0.19), residues: 813 loop : 0.14 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.014 0.001 TYR M 187 PHE 0.004 0.001 PHE L 582 TRP 0.006 0.001 TRP C 33 HIS 0.001 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00239 (17391) covalent geometry : angle 0.49548 (23613) SS BOND : bond 0.00103 ( 21) SS BOND : angle 0.57553 ( 42) hydrogen bonds : bond 0.22436 ( 516) hydrogen bonds : angle 8.99463 ( 1410) link_ALPHA1-3 : bond 0.00478 ( 6) link_ALPHA1-3 : angle 1.46144 ( 18) link_ALPHA1-6 : bond 0.00431 ( 3) link_ALPHA1-6 : angle 1.54262 ( 9) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 1.73258 ( 18) link_NAG-ASN : bond 0.00239 ( 6) link_NAG-ASN : angle 10.66703 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 467 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 139 ASP cc_start: 0.7335 (p0) cc_final: 0.7103 (p0) REVERT: C 80 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7187 (p90) REVERT: C 90 ASP cc_start: 0.6511 (m-30) cc_final: 0.6261 (m-30) outliers start: 11 outliers final: 3 residues processed: 476 average time/residue: 0.6006 time to fit residues: 315.3441 Evaluate side-chains 297 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 293 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain M residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS F 188 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN J 16 GLN J 28 ASN A 39 HIS B 521 GLN E 16 GLN E 55 HIS K 39 HIS L 521 GLN L 551 GLN ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN O 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.059701 restraints weight = 46174.724| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.25 r_work: 0.2969 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17433 Z= 0.242 Angle : 0.674 8.369 23718 Z= 0.340 Chirality : 0.045 0.182 2634 Planarity : 0.005 0.055 3000 Dihedral : 8.225 73.468 2783 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.53 % Allowed : 15.74 % Favored : 80.73 % 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: 0.20 (0.19), residues: 2127 helix: 0.58 (0.43), residues: 156 sheet: 0.41 (0.19), residues: 762 loop : -0.02 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 587 TYR 0.022 0.002 TYR E 51 PHE 0.019 0.001 PHE D 70 TRP 0.011 0.002 TRP K 104 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00540 (17391) covalent geometry : angle 0.66149 (23613) SS BOND : bond 0.00371 ( 21) SS BOND : angle 0.61182 ( 42) hydrogen bonds : bond 0.04608 ( 516) hydrogen bonds : angle 6.16522 ( 1410) link_ALPHA1-3 : bond 0.00471 ( 6) link_ALPHA1-3 : angle 2.42390 ( 18) link_ALPHA1-6 : bond 0.00090 ( 3) link_ALPHA1-6 : angle 2.45591 ( 9) link_BETA1-4 : bond 0.00116 ( 6) link_BETA1-4 : angle 2.61588 ( 18) link_NAG-ASN : bond 0.00156 ( 6) link_NAG-ASN : angle 2.67967 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 510 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8212 (tttp) REVERT: G 523 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7215 (tm-30) REVERT: G 545 GLU cc_start: 0.8427 (mp0) cc_final: 0.8174 (mp0) REVERT: H 139 ASP cc_start: 0.8461 (p0) cc_final: 0.8246 (p0) REVERT: I 46 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: I 95 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7606 (ttm) REVERT: A 56 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8230 (mmtm) REVERT: A 114 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8718 (mtpp) REVERT: B 523 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 548 MET cc_start: 0.8779 (ttm) cc_final: 0.8480 (ttm) REVERT: C 80 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6857 (p90) REVERT: C 213 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8632 (mm) REVERT: D 25 SER cc_start: 0.8926 (m) cc_final: 0.8323 (p) REVERT: D 46 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: D 75 ASP cc_start: 0.8669 (t0) cc_final: 0.8447 (p0) REVERT: D 80 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8626 (mtpm) REVERT: D 87 ASN cc_start: 0.8801 (t0) cc_final: 0.8555 (t0) REVERT: D 114 ARG cc_start: 0.7297 (mpt180) cc_final: 0.6955 (mpt180) REVERT: E 87 ASP cc_start: 0.8703 (m-30) cc_final: 0.8365 (m-30) REVERT: E 98 ARG cc_start: 0.8521 (mpp80) cc_final: 0.8227 (mpp80) REVERT: K 54 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7808 (ptm160) REVERT: K 120 GLU cc_start: 0.8348 (pm20) cc_final: 0.8112 (pm20) REVERT: L 523 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7287 (tm-30) REVERT: M 59 ASP cc_start: 0.8375 (t0) cc_final: 0.7975 (t0) REVERT: M 156 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8324 (ttp80) REVERT: N 28 THR cc_start: 0.8718 (m) cc_final: 0.8422 (t) REVERT: N 46 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7382 (tm-30) REVERT: N 67 ARG cc_start: 0.6769 (tpp-160) cc_final: 0.6383 (tpp-160) REVERT: N 87 ASN cc_start: 0.8825 (t0) cc_final: 0.8618 (t0) REVERT: N 95 MET cc_start: 0.8442 (mtp) cc_final: 0.7675 (ttm) REVERT: O 16 GLN cc_start: 0.8220 (pt0) cc_final: 0.7942 (pp30) REVERT: O 44 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8622 (p) REVERT: O 85 GLU cc_start: 0.8379 (tt0) cc_final: 0.8044 (tt0) REVERT: O 108 LYS cc_start: 0.8764 (tptm) cc_final: 0.8376 (tptp) outliers start: 63 outliers final: 24 residues processed: 358 average time/residue: 0.6359 time to fit residues: 250.1342 Evaluate side-chains 316 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN J 100 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 HIS E 100 GLN K 188 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059470 restraints weight = 46356.347| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.27 r_work: 0.2977 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17433 Z= 0.179 Angle : 0.613 7.844 23718 Z= 0.308 Chirality : 0.043 0.151 2634 Planarity : 0.004 0.034 3000 Dihedral : 7.779 65.856 2781 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.14 % Allowed : 17.14 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.18), residues: 2127 helix: 0.85 (0.42), residues: 156 sheet: 0.21 (0.19), residues: 741 loop : -0.07 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 114 TYR 0.026 0.001 TYR J 51 PHE 0.010 0.001 PHE N 70 TRP 0.009 0.001 TRP K 104 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00398 (17391) covalent geometry : angle 0.60421 (23613) SS BOND : bond 0.00280 ( 21) SS BOND : angle 0.41613 ( 42) hydrogen bonds : bond 0.03908 ( 516) hydrogen bonds : angle 5.67829 ( 1410) link_ALPHA1-3 : bond 0.00638 ( 6) link_ALPHA1-3 : angle 1.69709 ( 18) link_ALPHA1-6 : bond 0.00033 ( 3) link_ALPHA1-6 : angle 2.22356 ( 9) link_BETA1-4 : bond 0.00307 ( 6) link_BETA1-4 : angle 2.18662 ( 18) link_NAG-ASN : bond 0.00245 ( 6) link_NAG-ASN : angle 2.36555 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 127 ASP cc_start: 0.8203 (p0) cc_final: 0.7785 (p0) REVERT: G 523 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7147 (tm-30) REVERT: G 551 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: I 6 GLU cc_start: 0.8148 (mp0) cc_final: 0.7623 (mp0) REVERT: I 43 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8278 (tttm) REVERT: I 46 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7937 (tm-30) REVERT: I 87 ASN cc_start: 0.8888 (t0) cc_final: 0.8648 (t0) REVERT: I 95 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7503 (ttm) REVERT: I 114 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7528 (mtm110) REVERT: J 16 GLN cc_start: 0.8067 (pt0) cc_final: 0.7797 (pp30) REVERT: J 26 TYR cc_start: 0.9469 (p90) cc_final: 0.9192 (p90) REVERT: J 51 TYR cc_start: 0.8979 (p90) cc_final: 0.8778 (p90) REVERT: J 87 ASP cc_start: 0.8854 (m-30) cc_final: 0.8536 (m-30) REVERT: J 96 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8391 (mtm-85) REVERT: J 98 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8358 (mtm-85) REVERT: A 56 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8251 (mmtm) REVERT: A 114 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8724 (mtpp) REVERT: B 523 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 551 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (pp30) REVERT: C 54 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7327 (ttm170) REVERT: C 80 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6641 (p90) REVERT: C 213 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 25 SER cc_start: 0.8776 (m) cc_final: 0.8295 (p) REVERT: D 46 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7657 (tm-30) REVERT: D 80 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8739 (mtpm) REVERT: D 87 ASN cc_start: 0.8886 (t0) cc_final: 0.8579 (t0) REVERT: D 110 ASP cc_start: 0.7637 (m-30) cc_final: 0.7272 (m-30) REVERT: E 87 ASP cc_start: 0.8748 (m-30) cc_final: 0.8365 (m-30) REVERT: E 98 ARG cc_start: 0.8585 (mpp80) cc_final: 0.8348 (mpp80) REVERT: E 108 LYS cc_start: 0.8813 (tptm) cc_final: 0.8489 (tptp) REVERT: L 523 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7215 (tm-30) REVERT: L 545 GLU cc_start: 0.8523 (mp0) cc_final: 0.8322 (mp0) REVERT: M 11 LEU cc_start: 0.8823 (tp) cc_final: 0.8562 (tp) REVERT: M 59 ASP cc_start: 0.8410 (t0) cc_final: 0.8043 (t0) REVERT: M 156 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8395 (ttp80) REVERT: N 28 THR cc_start: 0.8694 (m) cc_final: 0.8383 (t) REVERT: N 46 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7533 (tm-30) REVERT: N 87 ASN cc_start: 0.8874 (t0) cc_final: 0.8632 (t0) REVERT: N 95 MET cc_start: 0.8527 (mtp) cc_final: 0.7765 (ttm) REVERT: O 16 GLN cc_start: 0.8247 (pt0) cc_final: 0.7951 (pp30) REVERT: O 44 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8665 (p) REVERT: O 85 GLU cc_start: 0.8349 (tt0) cc_final: 0.8107 (tt0) REVERT: O 87 ASP cc_start: 0.8795 (m-30) cc_final: 0.8506 (m-30) REVERT: O 108 LYS cc_start: 0.8789 (tptm) cc_final: 0.8418 (tptp) outliers start: 56 outliers final: 24 residues processed: 336 average time/residue: 0.6391 time to fit residues: 236.0135 Evaluate side-chains 313 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059893 restraints weight = 46203.671| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.25 r_work: 0.2979 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17433 Z= 0.148 Angle : 0.601 11.088 23718 Z= 0.299 Chirality : 0.042 0.156 2634 Planarity : 0.004 0.035 3000 Dihedral : 7.404 59.487 2781 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.59 % Allowed : 17.65 % Favored : 78.77 % 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: -0.02 (0.18), residues: 2127 helix: 1.07 (0.43), residues: 156 sheet: 0.08 (0.19), residues: 741 loop : -0.13 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 114 TYR 0.027 0.001 TYR E 51 PHE 0.008 0.001 PHE N 70 TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00330 (17391) covalent geometry : angle 0.59222 (23613) SS BOND : bond 0.00249 ( 21) SS BOND : angle 0.38912 ( 42) hydrogen bonds : bond 0.03437 ( 516) hydrogen bonds : angle 5.40140 ( 1410) link_ALPHA1-3 : bond 0.00729 ( 6) link_ALPHA1-3 : angle 1.86675 ( 18) link_ALPHA1-6 : bond 0.00105 ( 3) link_ALPHA1-6 : angle 2.12086 ( 9) link_BETA1-4 : bond 0.00413 ( 6) link_BETA1-4 : angle 2.18831 ( 18) link_NAG-ASN : bond 0.00135 ( 6) link_NAG-ASN : angle 2.07271 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8524 (mt0) cc_final: 0.7909 (mm-40) REVERT: F 54 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7941 (ptm-80) REVERT: F 56 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8200 (mmtm) REVERT: F 127 ASP cc_start: 0.8324 (p0) cc_final: 0.7873 (p0) REVERT: G 523 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7221 (tm-30) REVERT: G 551 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7518 (pp30) REVERT: H 90 ASP cc_start: 0.6600 (m-30) cc_final: 0.6370 (m-30) REVERT: I 6 GLU cc_start: 0.8107 (mp0) cc_final: 0.7571 (mp0) REVERT: I 43 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8162 (tttm) REVERT: I 46 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: I 87 ASN cc_start: 0.8833 (t0) cc_final: 0.8560 (t0) REVERT: I 95 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: I 114 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7467 (mtm110) REVERT: J 16 GLN cc_start: 0.8095 (pt0) cc_final: 0.7822 (pp30) REVERT: J 41 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8348 (mm) REVERT: J 51 TYR cc_start: 0.8958 (p90) cc_final: 0.8720 (p90) REVERT: J 81 GLN cc_start: 0.8951 (mp10) cc_final: 0.8624 (mp10) REVERT: J 87 ASP cc_start: 0.8874 (m-30) cc_final: 0.8538 (m-30) REVERT: J 94 ASP cc_start: 0.8088 (t0) cc_final: 0.7806 (t70) REVERT: J 96 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8333 (mtm-85) REVERT: A 56 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8233 (mmtm) REVERT: A 114 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8701 (mtpp) REVERT: B 523 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 551 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7516 (pp30) REVERT: C 13 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8691 (mmmm) REVERT: C 54 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7282 (ttm170) REVERT: C 59 ASP cc_start: 0.8300 (t0) cc_final: 0.8070 (t0) REVERT: C 213 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (mm) REVERT: D 3 GLN cc_start: 0.7941 (pp30) cc_final: 0.7623 (pp30) REVERT: D 25 SER cc_start: 0.8775 (m) cc_final: 0.8243 (p) REVERT: D 43 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8127 (mmmm) REVERT: D 46 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: D 87 ASN cc_start: 0.9042 (t0) cc_final: 0.8795 (t0) REVERT: D 95 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7489 (ttm) REVERT: D 110 ASP cc_start: 0.7616 (m-30) cc_final: 0.7366 (m-30) REVERT: E 87 ASP cc_start: 0.8742 (m-30) cc_final: 0.8413 (m-30) REVERT: E 94 ASP cc_start: 0.8120 (t0) cc_final: 0.7793 (t70) REVERT: E 98 ARG cc_start: 0.8532 (mpp80) cc_final: 0.8243 (mpp80) REVERT: E 108 LYS cc_start: 0.8825 (tptm) cc_final: 0.8398 (tptt) REVERT: K 77 THR cc_start: 0.8750 (p) cc_final: 0.8490 (t) REVERT: K 184 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8633 (pp) REVERT: L 523 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7273 (tm-30) REVERT: L 545 GLU cc_start: 0.8508 (mp0) cc_final: 0.8222 (mp0) REVERT: L 551 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7611 (pp30) REVERT: M 11 LEU cc_start: 0.8845 (tp) cc_final: 0.8601 (tp) REVERT: M 59 ASP cc_start: 0.8349 (t0) cc_final: 0.8025 (t0) REVERT: M 90 ASP cc_start: 0.6864 (m-30) cc_final: 0.6653 (m-30) REVERT: N 28 THR cc_start: 0.8614 (m) cc_final: 0.8294 (t) REVERT: N 43 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8415 (mmmm) REVERT: N 46 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7375 (tm-30) REVERT: N 87 ASN cc_start: 0.8938 (t0) cc_final: 0.8701 (t0) REVERT: N 95 MET cc_start: 0.8563 (mtp) cc_final: 0.7803 (ttm) REVERT: O 16 GLN cc_start: 0.8198 (pt0) cc_final: 0.7932 (pp30) REVERT: O 81 GLN cc_start: 0.8932 (mp10) cc_final: 0.8629 (mp10) REVERT: O 85 GLU cc_start: 0.8426 (tt0) cc_final: 0.8123 (tt0) REVERT: O 87 ASP cc_start: 0.8835 (m-30) cc_final: 0.8569 (m-30) REVERT: O 94 ASP cc_start: 0.8067 (t70) cc_final: 0.7586 (t70) REVERT: O 108 LYS cc_start: 0.8745 (tptm) cc_final: 0.8398 (tptp) outliers start: 64 outliers final: 29 residues processed: 333 average time/residue: 0.6839 time to fit residues: 249.9639 Evaluate side-chains 326 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain L residue 551 GLN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 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 = 0.3501 r_free = 0.3501 target = 0.076746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057954 restraints weight = 46299.070| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.26 r_work: 0.2928 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17433 Z= 0.212 Angle : 0.630 8.971 23718 Z= 0.315 Chirality : 0.043 0.167 2634 Planarity : 0.004 0.035 3000 Dihedral : 7.267 59.322 2781 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.03 % Allowed : 17.76 % Favored : 78.21 % 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: -0.16 (0.18), residues: 2127 helix: 1.23 (0.42), residues: 156 sheet: -0.10 (0.19), residues: 759 loop : -0.19 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 114 TYR 0.028 0.001 TYR E 51 PHE 0.008 0.001 PHE I 70 TRP 0.010 0.001 TRP H 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00472 (17391) covalent geometry : angle 0.62111 (23613) SS BOND : bond 0.00324 ( 21) SS BOND : angle 0.42226 ( 42) hydrogen bonds : bond 0.03489 ( 516) hydrogen bonds : angle 5.30689 ( 1410) link_ALPHA1-3 : bond 0.00467 ( 6) link_ALPHA1-3 : angle 1.95710 ( 18) link_ALPHA1-6 : bond 0.00238 ( 3) link_ALPHA1-6 : angle 2.34258 ( 9) link_BETA1-4 : bond 0.00249 ( 6) link_BETA1-4 : angle 2.28511 ( 18) link_NAG-ASN : bond 0.00370 ( 6) link_NAG-ASN : angle 2.25540 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8606 (mt0) cc_final: 0.8032 (mm-40) REVERT: F 54 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7998 (ptm160) REVERT: F 56 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8234 (mmtm) REVERT: F 127 ASP cc_start: 0.8383 (p0) cc_final: 0.7944 (p0) REVERT: G 523 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7208 (tm-30) REVERT: G 551 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: H 41 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: H 156 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8353 (ttp80) REVERT: I 6 GLU cc_start: 0.8069 (mp0) cc_final: 0.7480 (mp0) REVERT: I 43 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8125 (tttm) REVERT: I 46 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: I 87 ASN cc_start: 0.8885 (t0) cc_final: 0.8607 (t0) REVERT: I 95 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7521 (ttm) REVERT: I 114 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7452 (mtm110) REVERT: J 16 GLN cc_start: 0.8002 (pt0) cc_final: 0.7740 (pp30) REVERT: J 51 TYR cc_start: 0.9025 (p90) cc_final: 0.8818 (p90) REVERT: J 68 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8415 (tmmm) REVERT: J 81 GLN cc_start: 0.8936 (mp10) cc_final: 0.8555 (mp10) REVERT: J 87 ASP cc_start: 0.8870 (m-30) cc_final: 0.8535 (m-30) REVERT: J 96 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8343 (mtm-85) REVERT: A 56 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8246 (mmtm) REVERT: A 114 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8654 (mtpp) REVERT: B 523 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7063 (tm-30) REVERT: B 551 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7466 (pp30) REVERT: C 13 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8699 (mmmm) REVERT: C 46 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8639 (mt-10) REVERT: C 54 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7259 (ttm170) REVERT: C 213 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8631 (mm) REVERT: D 25 SER cc_start: 0.8838 (m) cc_final: 0.8280 (p) REVERT: D 46 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: D 67 ARG cc_start: 0.8036 (pmt-80) cc_final: 0.6617 (tpp80) REVERT: D 87 ASN cc_start: 0.8996 (t0) cc_final: 0.8753 (t0) REVERT: E 87 ASP cc_start: 0.8770 (m-30) cc_final: 0.8327 (m-30) REVERT: E 94 ASP cc_start: 0.8247 (t0) cc_final: 0.7891 (t70) REVERT: E 96 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8590 (mtm-85) REVERT: E 98 ARG cc_start: 0.8619 (mpp80) cc_final: 0.8247 (mpp80) REVERT: E 108 LYS cc_start: 0.8857 (tptm) cc_final: 0.8546 (tptp) REVERT: K 77 THR cc_start: 0.8814 (p) cc_final: 0.8562 (t) REVERT: K 184 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8753 (pp) REVERT: L 522 ASP cc_start: 0.7580 (t70) cc_final: 0.7227 (t0) REVERT: L 545 GLU cc_start: 0.8554 (mp0) cc_final: 0.8256 (mp0) REVERT: M 11 LEU cc_start: 0.8863 (tp) cc_final: 0.8612 (tp) REVERT: M 59 ASP cc_start: 0.8342 (t0) cc_final: 0.8047 (t0) REVERT: M 156 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8114 (ttp80) REVERT: N 13 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8492 (mm110) REVERT: N 46 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7551 (tm-30) REVERT: N 87 ASN cc_start: 0.8941 (t0) cc_final: 0.8721 (t0) REVERT: N 95 MET cc_start: 0.8627 (mtp) cc_final: 0.7759 (ttm) REVERT: O 16 GLN cc_start: 0.8267 (pt0) cc_final: 0.7991 (pp30) REVERT: O 81 GLN cc_start: 0.8923 (mp10) cc_final: 0.8669 (mp10) REVERT: O 85 GLU cc_start: 0.8367 (tt0) cc_final: 0.8042 (tt0) REVERT: O 94 ASP cc_start: 0.8176 (t70) cc_final: 0.7702 (t70) REVERT: O 96 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8578 (mtm-85) REVERT: O 108 LYS cc_start: 0.8799 (tptm) cc_final: 0.8464 (tptp) outliers start: 72 outliers final: 37 residues processed: 335 average time/residue: 0.6798 time to fit residues: 249.6846 Evaluate side-chains 323 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 96 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 204 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059200 restraints weight = 45582.370| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.25 r_work: 0.2967 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17433 Z= 0.135 Angle : 0.619 8.195 23718 Z= 0.309 Chirality : 0.043 0.154 2634 Planarity : 0.004 0.049 3000 Dihedral : 6.930 59.878 2781 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.25 % Allowed : 19.55 % Favored : 77.20 % 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: -0.14 (0.18), residues: 2127 helix: 1.32 (0.42), residues: 156 sheet: 0.04 (0.19), residues: 720 loop : -0.28 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 114 TYR 0.028 0.001 TYR E 51 PHE 0.008 0.001 PHE M 211 TRP 0.010 0.001 TRP I 47 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (17391) covalent geometry : angle 0.61186 (23613) SS BOND : bond 0.00203 ( 21) SS BOND : angle 0.32798 ( 42) hydrogen bonds : bond 0.03134 ( 516) hydrogen bonds : angle 5.20980 ( 1410) link_ALPHA1-3 : bond 0.00778 ( 6) link_ALPHA1-3 : angle 1.79818 ( 18) link_ALPHA1-6 : bond 0.00140 ( 3) link_ALPHA1-6 : angle 2.05441 ( 9) link_BETA1-4 : bond 0.00471 ( 6) link_BETA1-4 : angle 2.20966 ( 18) link_NAG-ASN : bond 0.00102 ( 6) link_NAG-ASN : angle 2.01921 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8603 (mt0) cc_final: 0.8034 (mm-40) REVERT: F 54 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8110 (ptm-80) REVERT: F 127 ASP cc_start: 0.8356 (p0) cc_final: 0.7929 (p0) REVERT: G 523 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7183 (tm-30) REVERT: G 540 GLU cc_start: 0.8697 (pm20) cc_final: 0.8452 (mp0) REVERT: H 41 PRO cc_start: 0.8263 (Cg_exo) cc_final: 0.8053 (Cg_endo) REVERT: H 89 GLU cc_start: 0.8198 (pp20) cc_final: 0.7928 (pp20) REVERT: H 90 ASP cc_start: 0.6889 (m-30) cc_final: 0.6687 (m-30) REVERT: I 6 GLU cc_start: 0.7998 (mp0) cc_final: 0.7503 (mp0) REVERT: I 46 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: I 87 ASN cc_start: 0.8859 (t0) cc_final: 0.8601 (t0) REVERT: I 95 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7583 (ttm) REVERT: I 114 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7562 (mtm110) REVERT: J 16 GLN cc_start: 0.7933 (pt0) cc_final: 0.7656 (pp30) REVERT: J 41 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8702 (mm) REVERT: J 68 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8289 (tmmm) REVERT: J 87 ASP cc_start: 0.8856 (m-30) cc_final: 0.8500 (m-30) REVERT: J 94 ASP cc_start: 0.8053 (t0) cc_final: 0.7789 (t70) REVERT: J 96 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8286 (mtm-85) REVERT: A 56 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8233 (mmtm) REVERT: A 114 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8702 (mtpp) REVERT: B 523 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 551 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7376 (pp30) REVERT: C 13 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8706 (mmmm) REVERT: C 34 MET cc_start: 0.9434 (mmm) cc_final: 0.9195 (tpt) REVERT: C 41 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8429 (pt0) REVERT: C 54 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7277 (ttm170) REVERT: C 59 ASP cc_start: 0.8327 (t0) cc_final: 0.8095 (t0) REVERT: C 213 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8568 (mm) REVERT: D 3 GLN cc_start: 0.8100 (pp30) cc_final: 0.7766 (pp30) REVERT: D 25 SER cc_start: 0.8798 (m) cc_final: 0.8303 (p) REVERT: D 46 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: D 67 ARG cc_start: 0.8061 (pmt-80) cc_final: 0.6618 (tpp80) REVERT: D 87 ASN cc_start: 0.9025 (t0) cc_final: 0.8807 (t0) REVERT: D 95 MET cc_start: 0.8169 (mtp) cc_final: 0.7620 (ttm) REVERT: E 81 GLN cc_start: 0.8736 (mp10) cc_final: 0.8300 (mp10) REVERT: E 87 ASP cc_start: 0.8793 (m-30) cc_final: 0.8365 (m-30) REVERT: E 94 ASP cc_start: 0.8191 (t0) cc_final: 0.7905 (t70) REVERT: E 98 ARG cc_start: 0.8527 (mpp80) cc_final: 0.8145 (mpp80) REVERT: E 108 LYS cc_start: 0.8861 (tptm) cc_final: 0.8547 (tptp) REVERT: E 109 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8583 (tp) REVERT: K 77 THR cc_start: 0.8740 (p) cc_final: 0.8498 (t) REVERT: K 156 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: K 184 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8698 (pp) REVERT: L 523 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7191 (tm-30) REVERT: L 540 GLU cc_start: 0.8717 (pm20) cc_final: 0.8497 (mp0) REVERT: L 545 GLU cc_start: 0.8512 (mp0) cc_final: 0.8198 (mp0) REVERT: M 11 LEU cc_start: 0.8878 (tp) cc_final: 0.8631 (tp) REVERT: M 46 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: M 54 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7144 (ttm170) REVERT: M 59 ASP cc_start: 0.8248 (t0) cc_final: 0.7938 (t0) REVERT: M 156 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8277 (ttp80) REVERT: N 13 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8465 (mm110) REVERT: N 46 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7465 (tm-30) REVERT: N 87 ASN cc_start: 0.8935 (t0) cc_final: 0.8708 (t0) REVERT: N 95 MET cc_start: 0.8625 (mtp) cc_final: 0.7738 (ttm) REVERT: O 16 GLN cc_start: 0.8186 (pt0) cc_final: 0.7924 (pp30) REVERT: O 41 LEU cc_start: 0.8839 (mm) cc_final: 0.8532 (mm) REVERT: O 81 GLN cc_start: 0.8936 (mp10) cc_final: 0.8558 (mp10) REVERT: O 85 GLU cc_start: 0.8414 (tt0) cc_final: 0.8124 (tt0) REVERT: O 94 ASP cc_start: 0.8079 (t70) cc_final: 0.7597 (t70) REVERT: O 108 LYS cc_start: 0.8787 (tptm) cc_final: 0.8422 (tptp) outliers start: 58 outliers final: 30 residues processed: 328 average time/residue: 0.6652 time to fit residues: 239.2843 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain K residue 156 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 0.0020 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 199 optimal weight: 0.0170 chunk 163 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059576 restraints weight = 45710.159| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.24 r_work: 0.2975 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17433 Z= 0.136 Angle : 0.625 8.476 23718 Z= 0.310 Chirality : 0.042 0.168 2634 Planarity : 0.004 0.039 3000 Dihedral : 6.727 57.445 2781 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.47 % Allowed : 20.00 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.13 (0.18), residues: 2127 helix: 1.43 (0.43), residues: 156 sheet: 0.03 (0.19), residues: 720 loop : -0.28 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 114 TYR 0.028 0.001 TYR E 51 PHE 0.007 0.001 PHE K 88 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (17391) covalent geometry : angle 0.61774 (23613) SS BOND : bond 0.00183 ( 21) SS BOND : angle 0.29604 ( 42) hydrogen bonds : bond 0.03036 ( 516) hydrogen bonds : angle 5.08250 ( 1410) link_ALPHA1-3 : bond 0.00728 ( 6) link_ALPHA1-3 : angle 1.81857 ( 18) link_ALPHA1-6 : bond 0.00148 ( 3) link_ALPHA1-6 : angle 2.00035 ( 9) link_BETA1-4 : bond 0.00431 ( 6) link_BETA1-4 : angle 2.24970 ( 18) link_NAG-ASN : bond 0.00095 ( 6) link_NAG-ASN : angle 1.95036 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8592 (mt0) cc_final: 0.8076 (mm-40) REVERT: F 56 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8151 (mmtm) REVERT: F 127 ASP cc_start: 0.8358 (p0) cc_final: 0.7928 (p0) REVERT: G 522 ASP cc_start: 0.7877 (m-30) cc_final: 0.7666 (t0) REVERT: G 523 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7324 (tm-30) REVERT: G 540 GLU cc_start: 0.8692 (pm20) cc_final: 0.8408 (mp0) REVERT: H 41 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: H 90 ASP cc_start: 0.6788 (m-30) cc_final: 0.6530 (m-30) REVERT: I 6 GLU cc_start: 0.7925 (mp0) cc_final: 0.7424 (mp0) REVERT: I 43 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8304 (tttm) REVERT: I 46 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: I 87 ASN cc_start: 0.8842 (t0) cc_final: 0.8589 (t0) REVERT: I 95 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: I 114 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7550 (mtm110) REVERT: J 16 GLN cc_start: 0.8034 (pt0) cc_final: 0.7813 (pp30) REVERT: J 87 ASP cc_start: 0.8829 (m-30) cc_final: 0.8492 (m-30) REVERT: J 94 ASP cc_start: 0.8055 (t0) cc_final: 0.7766 (t70) REVERT: J 96 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8277 (mtm-85) REVERT: A 56 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8223 (mmtm) REVERT: A 114 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8667 (mtpp) REVERT: B 523 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 551 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: C 13 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8721 (mmmm) REVERT: C 34 MET cc_start: 0.9394 (mmm) cc_final: 0.9160 (tpt) REVERT: C 40 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7689 (tpp80) REVERT: C 41 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.7898 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7898 (mm110) REVERT: C 46 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8413 (pt0) REVERT: C 54 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.6700 (tpp80) REVERT: C 89 GLU cc_start: 0.8227 (pp20) cc_final: 0.7895 (pp20) REVERT: C 213 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8525 (mm) REVERT: D 3 GLN cc_start: 0.8126 (pp30) cc_final: 0.7865 (pp30) REVERT: D 4 LEU cc_start: 0.8125 (mp) cc_final: 0.7855 (mp) REVERT: D 25 SER cc_start: 0.8860 (m) cc_final: 0.8307 (p) REVERT: D 39 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 46 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: D 67 ARG cc_start: 0.8097 (pmt-80) cc_final: 0.6687 (tpp80) REVERT: D 78 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9072 (pmtt) REVERT: D 95 MET cc_start: 0.8204 (mtp) cc_final: 0.7544 (ttm) REVERT: E 68 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8179 (tmmm) REVERT: E 81 GLN cc_start: 0.8891 (mp10) cc_final: 0.8394 (mp10) REVERT: E 87 ASP cc_start: 0.8787 (m-30) cc_final: 0.8335 (m-30) REVERT: E 94 ASP cc_start: 0.8174 (t0) cc_final: 0.7905 (t70) REVERT: E 108 LYS cc_start: 0.8857 (tptm) cc_final: 0.8536 (tptp) REVERT: K 77 THR cc_start: 0.8708 (p) cc_final: 0.8463 (t) REVERT: K 184 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (pp) REVERT: L 523 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7312 (tm-30) REVERT: L 540 GLU cc_start: 0.8693 (pm20) cc_final: 0.8425 (mp0) REVERT: L 545 GLU cc_start: 0.8493 (mp0) cc_final: 0.8184 (mp0) REVERT: M 11 LEU cc_start: 0.8885 (tp) cc_final: 0.8666 (tp) REVERT: M 43 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8212 (mm110) REVERT: M 46 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8680 (pt0) REVERT: M 59 ASP cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) REVERT: M 156 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8243 (ttp80) REVERT: N 13 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8392 (mm110) REVERT: N 39 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8380 (tm-30) REVERT: N 46 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: N 85 MET cc_start: 0.8208 (mtt) cc_final: 0.7967 (mmm) REVERT: N 87 ASN cc_start: 0.8915 (t0) cc_final: 0.8704 (t0) REVERT: N 95 MET cc_start: 0.8596 (mtp) cc_final: 0.7690 (ttm) REVERT: O 16 GLN cc_start: 0.8172 (pt0) cc_final: 0.7913 (pp30) REVERT: O 41 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (mm) REVERT: O 81 GLN cc_start: 0.8897 (mp10) cc_final: 0.8572 (mp10) REVERT: O 85 GLU cc_start: 0.8379 (tt0) cc_final: 0.8049 (tt0) REVERT: O 94 ASP cc_start: 0.8077 (t70) cc_final: 0.7613 (t70) REVERT: O 108 LYS cc_start: 0.8777 (tptm) cc_final: 0.8448 (tptp) outliers start: 62 outliers final: 32 residues processed: 334 average time/residue: 0.6301 time to fit residues: 230.7399 Evaluate side-chains 332 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN J 100 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058781 restraints weight = 45801.027| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.33 r_work: 0.2952 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17433 Z= 0.186 Angle : 0.651 8.710 23718 Z= 0.324 Chirality : 0.043 0.177 2634 Planarity : 0.004 0.047 3000 Dihedral : 6.699 56.684 2781 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.14 % Allowed : 20.84 % Favored : 76.02 % 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: -0.17 (0.18), residues: 2127 helix: 1.45 (0.42), residues: 156 sheet: -0.03 (0.19), residues: 723 loop : -0.30 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 114 TYR 0.030 0.001 TYR J 51 PHE 0.008 0.001 PHE K 88 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00420 (17391) covalent geometry : angle 0.64300 (23613) SS BOND : bond 0.00240 ( 21) SS BOND : angle 0.31866 ( 42) hydrogen bonds : bond 0.03170 ( 516) hydrogen bonds : angle 5.04963 ( 1410) link_ALPHA1-3 : bond 0.00601 ( 6) link_ALPHA1-3 : angle 1.91592 ( 18) link_ALPHA1-6 : bond 0.00095 ( 3) link_ALPHA1-6 : angle 2.15089 ( 9) link_BETA1-4 : bond 0.00274 ( 6) link_BETA1-4 : angle 2.39154 ( 18) link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.05842 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8579 (mt0) cc_final: 0.8056 (mm-40) REVERT: F 56 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8136 (mmtm) REVERT: F 127 ASP cc_start: 0.8415 (p0) cc_final: 0.8012 (p0) REVERT: G 522 ASP cc_start: 0.7959 (m-30) cc_final: 0.7715 (t0) REVERT: G 523 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 540 GLU cc_start: 0.8712 (pm20) cc_final: 0.8386 (mp0) REVERT: H 41 PRO cc_start: 0.8526 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: I 6 GLU cc_start: 0.7911 (mp0) cc_final: 0.7384 (mp0) REVERT: I 43 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8366 (tttm) REVERT: I 46 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: I 87 ASN cc_start: 0.8853 (t0) cc_final: 0.8601 (t0) REVERT: I 95 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7586 (ttm) REVERT: I 114 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7548 (mtm110) REVERT: J 87 ASP cc_start: 0.8846 (m-30) cc_final: 0.8491 (m-30) REVERT: J 94 ASP cc_start: 0.8129 (t0) cc_final: 0.7862 (t70) REVERT: J 96 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8265 (mtm-85) REVERT: A 114 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8588 (mtpp) REVERT: A 156 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 523 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 551 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: C 13 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8736 (mmmm) REVERT: C 40 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7695 (tpp80) REVERT: C 41 PRO cc_start: 0.8631 (Cg_exo) cc_final: 0.8412 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8642 (mt-10) REVERT: C 54 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7394 (ttp-170) REVERT: C 59 ASP cc_start: 0.8344 (t0) cc_final: 0.8073 (t0) REVERT: C 89 GLU cc_start: 0.8228 (pp20) cc_final: 0.7889 (pp20) REVERT: C 213 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8578 (mm) REVERT: D 3 GLN cc_start: 0.8187 (pp30) cc_final: 0.7927 (pp30) REVERT: D 25 SER cc_start: 0.8820 (m) cc_final: 0.8290 (p) REVERT: D 39 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 46 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: D 78 LYS cc_start: 0.9302 (mtmm) cc_final: 0.9043 (pmtt) REVERT: D 95 MET cc_start: 0.8229 (mtp) cc_final: 0.7505 (ttm) REVERT: E 68 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8186 (tmmm) REVERT: E 81 GLN cc_start: 0.8895 (mp10) cc_final: 0.8416 (mp10) REVERT: E 87 ASP cc_start: 0.8788 (m-30) cc_final: 0.8356 (m-30) REVERT: E 94 ASP cc_start: 0.8201 (t0) cc_final: 0.7938 (t70) REVERT: E 108 LYS cc_start: 0.8831 (tptm) cc_final: 0.8508 (tptp) REVERT: K 44 GLN cc_start: 0.8338 (mt0) cc_final: 0.7748 (mm-40) REVERT: K 184 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8675 (pp) REVERT: L 523 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7287 (tm-30) REVERT: L 540 GLU cc_start: 0.8696 (pm20) cc_final: 0.8423 (mp0) REVERT: L 545 GLU cc_start: 0.8498 (mp0) cc_final: 0.8149 (mp0) REVERT: M 43 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8237 (mm110) REVERT: M 59 ASP cc_start: 0.8263 (t0) cc_final: 0.7919 (t0) REVERT: M 156 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8259 (ttp80) REVERT: M 213 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8543 (mm) REVERT: N 13 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8517 (mm110) REVERT: N 39 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8384 (tm-30) REVERT: N 46 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: N 85 MET cc_start: 0.8260 (mtt) cc_final: 0.8060 (mtt) REVERT: N 87 ASN cc_start: 0.8958 (t0) cc_final: 0.8752 (t0) REVERT: N 95 MET cc_start: 0.8608 (mtp) cc_final: 0.7555 (ttm) REVERT: O 16 GLN cc_start: 0.8182 (pt0) cc_final: 0.7937 (pp30) REVERT: O 81 GLN cc_start: 0.8904 (mp10) cc_final: 0.8529 (mp10) REVERT: O 85 GLU cc_start: 0.8406 (tt0) cc_final: 0.8101 (tt0) REVERT: O 94 ASP cc_start: 0.8135 (t70) cc_final: 0.7684 (t70) REVERT: O 96 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8545 (mtm-85) REVERT: O 108 LYS cc_start: 0.8771 (tptm) cc_final: 0.8435 (tptp) outliers start: 56 outliers final: 33 residues processed: 322 average time/residue: 0.6148 time to fit residues: 217.4170 Evaluate side-chains 326 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 96 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 551 GLN J 28 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057952 restraints weight = 45821.267| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.33 r_work: 0.2936 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17433 Z= 0.205 Angle : 0.671 9.238 23718 Z= 0.335 Chirality : 0.043 0.181 2634 Planarity : 0.004 0.053 3000 Dihedral : 6.661 56.389 2781 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.75 % Allowed : 21.34 % Favored : 75.91 % 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: -0.23 (0.18), residues: 2127 helix: 1.44 (0.42), residues: 156 sheet: -0.23 (0.18), residues: 768 loop : -0.22 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 114 TYR 0.028 0.001 TYR E 51 PHE 0.007 0.001 PHE K 88 TRP 0.009 0.001 TRP I 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00462 (17391) covalent geometry : angle 0.66323 (23613) SS BOND : bond 0.00265 ( 21) SS BOND : angle 0.34921 ( 42) hydrogen bonds : bond 0.03234 ( 516) hydrogen bonds : angle 5.07135 ( 1410) link_ALPHA1-3 : bond 0.00574 ( 6) link_ALPHA1-3 : angle 1.91002 ( 18) link_ALPHA1-6 : bond 0.00184 ( 3) link_ALPHA1-6 : angle 2.21147 ( 9) link_BETA1-4 : bond 0.00228 ( 6) link_BETA1-4 : angle 2.46115 ( 18) link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.15565 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8603 (mt0) cc_final: 0.8079 (mm-40) REVERT: F 56 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8148 (mmtm) REVERT: F 127 ASP cc_start: 0.8430 (p0) cc_final: 0.8032 (p0) REVERT: G 523 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7266 (tm-30) REVERT: G 540 GLU cc_start: 0.8719 (pm20) cc_final: 0.8386 (mp0) REVERT: G 551 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7329 (pp30) REVERT: H 41 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: H 54 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.7231 (ttp-170) REVERT: H 146 HIS cc_start: 0.7429 (m90) cc_final: 0.7169 (m90) REVERT: H 156 ARG cc_start: 0.8888 (tmt90) cc_final: 0.8532 (ttp80) REVERT: I 6 GLU cc_start: 0.7963 (mp0) cc_final: 0.7439 (mp0) REVERT: I 46 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: I 87 ASN cc_start: 0.8835 (t0) cc_final: 0.8584 (t0) REVERT: I 95 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: I 114 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7576 (mtm110) REVERT: J 87 ASP cc_start: 0.8833 (m-30) cc_final: 0.8496 (m-30) REVERT: J 94 ASP cc_start: 0.8144 (t0) cc_final: 0.7872 (t70) REVERT: J 96 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8265 (mtm-85) REVERT: A 56 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8203 (mmtm) REVERT: A 114 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8592 (mtpp) REVERT: A 156 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8547 (mm-30) REVERT: B 523 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 551 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7449 (pp30) REVERT: C 13 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8742 (mmmm) REVERT: C 46 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8689 (mt-10) REVERT: C 54 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7390 (ttp-170) REVERT: C 59 ASP cc_start: 0.8407 (t0) cc_final: 0.8136 (t0) REVERT: C 89 GLU cc_start: 0.8220 (pp20) cc_final: 0.7928 (pp20) REVERT: C 213 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8618 (mm) REVERT: D 3 GLN cc_start: 0.8223 (pp30) cc_final: 0.7961 (pp30) REVERT: D 4 LEU cc_start: 0.8230 (mp) cc_final: 0.8010 (mp) REVERT: D 25 SER cc_start: 0.8875 (m) cc_final: 0.8331 (p) REVERT: D 39 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 46 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 78 LYS cc_start: 0.9321 (mtmm) cc_final: 0.9078 (pmtt) REVERT: D 95 MET cc_start: 0.8273 (mtp) cc_final: 0.7519 (ttm) REVERT: D 114 ARG cc_start: 0.6946 (mpt180) cc_final: 0.6676 (mpt180) REVERT: E 68 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8200 (tmmm) REVERT: E 81 GLN cc_start: 0.8905 (mp10) cc_final: 0.8469 (mp10) REVERT: E 87 ASP cc_start: 0.8845 (m-30) cc_final: 0.8425 (m-30) REVERT: E 94 ASP cc_start: 0.8223 (t0) cc_final: 0.7962 (t70) REVERT: E 108 LYS cc_start: 0.8838 (tptm) cc_final: 0.8531 (tptp) REVERT: K 44 GLN cc_start: 0.8368 (mt0) cc_final: 0.7810 (mm-40) REVERT: K 184 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8724 (pp) REVERT: L 523 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7361 (tm-30) REVERT: L 540 GLU cc_start: 0.8694 (pm20) cc_final: 0.8424 (mp0) REVERT: L 545 GLU cc_start: 0.8489 (mp0) cc_final: 0.8204 (mp0) REVERT: M 43 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8285 (mm110) REVERT: M 59 ASP cc_start: 0.8264 (t0) cc_final: 0.7974 (t0) REVERT: M 156 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8288 (ttp80) REVERT: M 213 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8565 (mm) REVERT: N 13 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8518 (mm110) REVERT: N 39 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8400 (tm-30) REVERT: N 46 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: N 95 MET cc_start: 0.8613 (mtp) cc_final: 0.7579 (ttm) REVERT: O 16 GLN cc_start: 0.8190 (pt0) cc_final: 0.7932 (pp30) REVERT: O 81 GLN cc_start: 0.8918 (mp10) cc_final: 0.8524 (mp10) REVERT: O 85 GLU cc_start: 0.8432 (tt0) cc_final: 0.8120 (tt0) REVERT: O 94 ASP cc_start: 0.8185 (t70) cc_final: 0.7718 (t70) REVERT: O 96 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8545 (mtm-85) REVERT: O 108 LYS cc_start: 0.8792 (tptm) cc_final: 0.8463 (tptp) outliers start: 49 outliers final: 30 residues processed: 318 average time/residue: 0.6172 time to fit residues: 215.5875 Evaluate side-chains 323 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 96 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 206 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 551 GLN J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 551 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 GLN N 86 ASN N 103 GLN ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058932 restraints weight = 45606.470| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.24 r_work: 0.2970 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17433 Z= 0.153 Angle : 0.668 9.506 23718 Z= 0.333 Chirality : 0.043 0.176 2634 Planarity : 0.004 0.057 3000 Dihedral : 6.417 55.778 2779 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 21.68 % Favored : 75.63 % 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: -0.20 (0.18), residues: 2127 helix: 1.64 (0.42), residues: 153 sheet: -0.20 (0.19), residues: 759 loop : -0.23 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 114 TYR 0.030 0.001 TYR J 51 PHE 0.015 0.001 PHE N 70 TRP 0.010 0.001 TRP I 47 HIS 0.007 0.001 HIS G 549 Details of bonding type rmsd covalent geometry : bond 0.00347 (17391) covalent geometry : angle 0.66022 (23613) SS BOND : bond 0.00188 ( 21) SS BOND : angle 0.36055 ( 42) hydrogen bonds : bond 0.03053 ( 516) hydrogen bonds : angle 5.03032 ( 1410) link_ALPHA1-3 : bond 0.00740 ( 6) link_ALPHA1-3 : angle 1.80752 ( 18) link_ALPHA1-6 : bond 0.00070 ( 3) link_ALPHA1-6 : angle 2.03902 ( 9) link_BETA1-4 : bond 0.00387 ( 6) link_BETA1-4 : angle 2.42147 ( 18) link_NAG-ASN : bond 0.00116 ( 6) link_NAG-ASN : angle 2.03666 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8625 (mt0) cc_final: 0.8068 (mm-40) REVERT: F 56 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8159 (mmtm) REVERT: F 127 ASP cc_start: 0.8350 (p0) cc_final: 0.7926 (p0) REVERT: G 522 ASP cc_start: 0.7880 (m-30) cc_final: 0.7625 (t0) REVERT: G 523 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7386 (tm-30) REVERT: G 540 GLU cc_start: 0.8738 (pm20) cc_final: 0.8424 (mp0) REVERT: G 551 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: H 41 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8242 (Cg_endo) REVERT: H 54 ARG cc_start: 0.7520 (ttp-170) cc_final: 0.7029 (ttm110) REVERT: H 80 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: H 146 HIS cc_start: 0.7401 (m90) cc_final: 0.7151 (m90) REVERT: H 156 ARG cc_start: 0.8867 (tmt90) cc_final: 0.8538 (ttp80) REVERT: I 6 GLU cc_start: 0.7889 (mp0) cc_final: 0.7412 (mp0) REVERT: I 46 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: I 87 ASN cc_start: 0.8822 (t0) cc_final: 0.8588 (t0) REVERT: I 95 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: I 114 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7616 (mtm110) REVERT: J 87 ASP cc_start: 0.8817 (m-30) cc_final: 0.8473 (m-30) REVERT: J 94 ASP cc_start: 0.8129 (t0) cc_final: 0.7881 (t70) REVERT: J 96 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8294 (mtm-85) REVERT: A 56 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8229 (mmtm) REVERT: A 114 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8668 (mtpp) REVERT: A 156 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 523 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 551 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: C 13 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8728 (mmmm) REVERT: C 34 MET cc_start: 0.9422 (mmm) cc_final: 0.9189 (tpt) REVERT: C 40 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7780 (tpp80) REVERT: C 43 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7894 (mm110) REVERT: C 46 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8675 (mt-10) REVERT: C 54 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.6701 (tpp80) REVERT: C 59 ASP cc_start: 0.8451 (t0) cc_final: 0.8140 (t0) REVERT: C 213 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8606 (mm) REVERT: D 4 LEU cc_start: 0.8230 (mp) cc_final: 0.7982 (mp) REVERT: D 39 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 46 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 78 LYS cc_start: 0.9278 (mtmm) cc_final: 0.9063 (pmtt) REVERT: D 95 MET cc_start: 0.8291 (mtp) cc_final: 0.7655 (ttm) REVERT: D 114 ARG cc_start: 0.7048 (mpt180) cc_final: 0.6772 (mpt180) REVERT: E 68 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8194 (tmmm) REVERT: E 81 GLN cc_start: 0.8903 (mp10) cc_final: 0.8471 (mp10) REVERT: E 87 ASP cc_start: 0.8865 (m-30) cc_final: 0.8452 (m-30) REVERT: E 94 ASP cc_start: 0.8156 (t0) cc_final: 0.7903 (t70) REVERT: E 108 LYS cc_start: 0.8869 (tptm) cc_final: 0.8566 (tptp) REVERT: K 77 THR cc_start: 0.8779 (p) cc_final: 0.8550 (t) REVERT: K 184 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8722 (pp) REVERT: L 523 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7372 (tm-30) REVERT: L 540 GLU cc_start: 0.8680 (pm20) cc_final: 0.8403 (mp0) REVERT: L 545 GLU cc_start: 0.8469 (mp0) cc_final: 0.8201 (mp0) REVERT: L 551 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: M 11 LEU cc_start: 0.8882 (tp) cc_final: 0.8669 (tt) REVERT: M 43 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8231 (mm110) REVERT: M 59 ASP cc_start: 0.8255 (t0) cc_final: 0.7986 (t0) REVERT: M 156 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8299 (ttp80) REVERT: M 213 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8607 (mm) REVERT: N 13 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8470 (mm110) REVERT: N 39 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8454 (tm-30) REVERT: N 46 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: N 95 MET cc_start: 0.8622 (mtp) cc_final: 0.7636 (ttm) REVERT: O 16 GLN cc_start: 0.8041 (pt0) cc_final: 0.7791 (pp30) REVERT: O 81 GLN cc_start: 0.8892 (mp10) cc_final: 0.8500 (mp10) REVERT: O 85 GLU cc_start: 0.8423 (tt0) cc_final: 0.8121 (tt0) REVERT: O 94 ASP cc_start: 0.8085 (t70) cc_final: 0.7656 (t70) REVERT: O 108 LYS cc_start: 0.8789 (tptm) cc_final: 0.8468 (tptp) outliers start: 48 outliers final: 30 residues processed: 318 average time/residue: 0.6113 time to fit residues: 213.0458 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain L residue 551 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 172 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 549 HIS G 551 GLN J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 551 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058923 restraints weight = 45586.780| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.25 r_work: 0.2970 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17433 Z= 0.156 Angle : 0.673 9.636 23718 Z= 0.336 Chirality : 0.043 0.174 2634 Planarity : 0.004 0.057 3000 Dihedral : 6.371 55.268 2779 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.63 % Allowed : 21.90 % Favored : 75.46 % 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: -0.20 (0.18), residues: 2127 helix: 1.62 (0.42), residues: 153 sheet: -0.16 (0.19), residues: 753 loop : -0.26 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 114 TYR 0.029 0.001 TYR E 51 PHE 0.010 0.001 PHE N 70 TRP 0.010 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00356 (17391) covalent geometry : angle 0.66565 (23613) SS BOND : bond 0.00188 ( 21) SS BOND : angle 0.34316 ( 42) hydrogen bonds : bond 0.03050 ( 516) hydrogen bonds : angle 5.02024 ( 1410) link_ALPHA1-3 : bond 0.00715 ( 6) link_ALPHA1-3 : angle 1.82843 ( 18) link_ALPHA1-6 : bond 0.00064 ( 3) link_ALPHA1-6 : angle 2.03576 ( 9) link_BETA1-4 : bond 0.00385 ( 6) link_BETA1-4 : angle 2.43186 ( 18) link_NAG-ASN : bond 0.00096 ( 6) link_NAG-ASN : angle 2.01696 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5681.38 seconds wall clock time: 97 minutes 43.74 seconds (5863.74 seconds total)