Starting phenix.real_space_refine on Sat Jul 4 14:34:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpm_27638/07_2026/8dpm_27638.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "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 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 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 chiralities: 1 Time building chain proxies: 3.66, 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: 1.67 Conformation dependent library (CDL) restraints added in 645.5 milliseconds 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: 0.72 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: 3.01 Time building geometry restraints manager: 2.10 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 - 15.57: 9528 15.57 - 31.14: 402 31.14 - 46.71: 68 46.71 - 62.28: 7 62.28 - 77.85: 9 Dihedral angle restraints: 10014 sinusoidal: 3882 harmonic: 6132 Sorted by residual: dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -113.25 27.25 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CB CYS F 121 " pdb=" SG CYS F 121 " pdb=" SG CYS F 147 " pdb=" CB CYS F 147 " ideal model delta sinusoidal sigma weight residual -86.00 -113.20 27.20 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CB CYS K 121 " pdb=" SG CYS K 121 " pdb=" SG CYS K 147 " pdb=" CB CYS K 147 " ideal model delta sinusoidal sigma weight residual -86.00 -112.82 26.82 1 1.00e+01 1.00e-02 1.03e+01 ... (remaining 10011 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: 0.05 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'C' selection = chain '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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 8.892 77.854 6069 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 are 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/Z covalent geometry : bond 0.00239 / 0.12 (17391) covalent geometry : angle 0.49548 / 0.25 (23613) SS BOND : bond 0.00103 / 0.05 ( 21) SS BOND : angle 0.57553 / 0.36 ( 42) hydrogen bonds : bond 0.22436 / 15.19 ( 516) hydrogen bonds : angle 8.99463 / 6.34 ( 1410) link_ALPHA1-3 : bond 0.00478 / 0.25 ( 6) link_ALPHA1-3 : angle 1.46144 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00431 / 0.20 ( 3) link_ALPHA1-6 : angle 1.54262 / 0.83 ( 9) link_BETA1-4 : bond 0.00453 / 0.24 ( 6) link_BETA1-4 : angle 1.73258 / 1.06 ( 18) link_NAG-ASN : bond 0.00239 / 0.11 ( 6) link_NAG-ASN : angle 10.66703 / 8.36 ( 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 : 0.665 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: 0.6381 time to fit residues: 336.0958 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 : 0.664 ------------------------------------------------------------------------------- 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... 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 28 ASN E 55 HIS K 39 HIS L 521 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 = 0.3540 r_free = 0.3540 target = 0.078451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059530 restraints weight = 46159.106| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.25 r_work: 0.2965 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17433 Z= 0.244 Angle : 0.670 8.450 23718 Z= 0.339 Chirality : 0.044 0.173 2634 Planarity : 0.005 0.056 3000 Dihedral : 4.146 54.358 2366 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.70 % Allowed : 15.69 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 2127 helix: 0.52 (0.42), residues: 156 sheet: 0.39 (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 0.023 0.002 TYR E 51 PHE 0.021 0.001 PHE C 200 TRP 0.012 0.002 TRP M 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (17391) covalent geometry : angle 0.66049 / 0.34 (23613) SS BOND : bond 0.00340 / 0.21 ( 21) SS BOND : angle 0.64152 / 0.39 ( 42) hydrogen bonds : bond 0.04427 / 3.01 ( 516) hydrogen bonds : angle 6.11304 / 4.34 ( 1410) link_ALPHA1-3 : bond 0.00100 / 0.06 ( 6) link_ALPHA1-3 : angle 1.95240 / 1.21 ( 18) link_ALPHA1-6 : bond 0.00018 / 0.01 ( 3) link_ALPHA1-6 : angle 2.82394 / 1.51 ( 9) link_BETA1-4 : bond 0.00279 / 0.16 ( 6) link_BETA1-4 : angle 2.23738 / 1.38 ( 18) link_NAG-ASN : bond 0.00049 / 0.03 ( 6) link_NAG-ASN : angle 2.46621 / 1.62 ( 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 394 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 510 LYS cc_start: 0.8853 (mtpm) cc_final: 0.8209 (tttp) REVERT: G 523 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7232 (tm-30) REVERT: G 545 GLU cc_start: 0.8416 (mp0) cc_final: 0.8129 (mp0) REVERT: H 139 ASP cc_start: 0.8466 (p0) cc_final: 0.8249 (p0) REVERT: I 46 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: I 95 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7589 (ttm) REVERT: A 56 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8239 (mmtm) REVERT: A 114 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8712 (mtpp) REVERT: B 523 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 548 MET cc_start: 0.8779 (ttm) cc_final: 0.8482 (ttm) REVERT: C 80 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6876 (p90) REVERT: C 213 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 25 SER cc_start: 0.8881 (m) cc_final: 0.8326 (p) REVERT: D 46 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: D 75 ASP cc_start: 0.8664 (t0) cc_final: 0.8450 (p0) REVERT: D 80 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8647 (mtpm) REVERT: D 87 ASN cc_start: 0.8833 (t0) cc_final: 0.8592 (t0) REVERT: D 114 ARG cc_start: 0.7307 (mpt180) cc_final: 0.6963 (mpt180) REVERT: E 87 ASP cc_start: 0.8722 (m-30) cc_final: 0.8396 (m-30) REVERT: E 98 ARG cc_start: 0.8561 (mpp80) cc_final: 0.8256 (mpp80) REVERT: K 54 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7847 (ptm160) REVERT: K 120 GLU cc_start: 0.8356 (pm20) cc_final: 0.8119 (pm20) REVERT: L 523 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7300 (tm-30) REVERT: M 59 ASP cc_start: 0.8405 (t0) cc_final: 0.7992 (t0) REVERT: M 156 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8360 (ttp80) REVERT: N 28 THR cc_start: 0.8726 (m) cc_final: 0.8433 (t) REVERT: N 46 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7420 (tm-30) REVERT: N 87 ASN cc_start: 0.8840 (t0) cc_final: 0.8634 (t0) REVERT: N 95 MET cc_start: 0.8452 (mtp) cc_final: 0.7697 (ttm) REVERT: O 16 GLN cc_start: 0.8184 (pt0) cc_final: 0.7964 (pp30) REVERT: O 44 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8627 (p) REVERT: O 85 GLU cc_start: 0.8400 (tt0) cc_final: 0.8082 (tt0) REVERT: O 108 LYS cc_start: 0.8743 (tptm) cc_final: 0.8346 (tptp) outliers start: 66 outliers final: 25 residues processed: 359 average time/residue: 0.6017 time to fit residues: 238.6006 Evaluate side-chains 317 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 B residue 545 GLU Chi-restraints excluded: chain C residue 4 LEU 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: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 177 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 161 optimal weight: 0.0070 chunk 141 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 149 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 28 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060177 restraints weight = 46263.054| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.28 r_work: 0.2994 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17433 Z= 0.146 Angle : 0.604 8.398 23718 Z= 0.303 Chirality : 0.042 0.155 2634 Planarity : 0.004 0.034 3000 Dihedral : 4.121 56.727 2364 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.14 % Allowed : 17.31 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2127 helix: 0.81 (0.42), residues: 156 sheet: 0.23 (0.19), residues: 741 loop : -0.06 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 114 TYR 0.025 0.001 TYR J 51 PHE 0.009 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/Z covalent geometry : bond 0.00325 / 0.15 (17391) covalent geometry : angle 0.59665 / 0.30 (23613) SS BOND : bond 0.00239 / 0.15 ( 21) SS BOND : angle 0.39088 / 0.22 ( 42) hydrogen bonds : bond 0.03799 / 2.58 ( 516) hydrogen bonds : angle 5.68603 / 4.04 ( 1410) link_ALPHA1-3 : bond 0.00483 / 0.26 ( 6) link_ALPHA1-3 : angle 1.44504 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00374 / 0.17 ( 3) link_ALPHA1-6 : angle 2.23321 / 1.20 ( 9) link_BETA1-4 : bond 0.00383 / 0.22 ( 6) link_BETA1-4 : angle 1.82875 / 1.08 ( 18) link_NAG-ASN : bond 0.00135 / 0.07 ( 6) link_NAG-ASN : angle 2.15724 / 1.44 ( 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 365 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8484 (mt0) cc_final: 0.7815 (mm-40) REVERT: F 100 GLU cc_start: 0.8758 (mp0) cc_final: 0.8547 (mp0) REVERT: F 127 ASP cc_start: 0.8220 (p0) cc_final: 0.7795 (p0) REVERT: G 523 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7166 (tm-30) REVERT: G 551 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: H 139 ASP cc_start: 0.8490 (p0) cc_final: 0.8281 (p0) REVERT: I 6 GLU cc_start: 0.8162 (mp0) cc_final: 0.7657 (mp0) REVERT: I 43 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8289 (tttm) REVERT: I 46 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7954 (tm-30) REVERT: I 87 ASN cc_start: 0.8807 (t0) cc_final: 0.8588 (t0) REVERT: I 95 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7627 (ttm) REVERT: I 114 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7440 (mtm110) REVERT: J 16 GLN cc_start: 0.8034 (pt0) cc_final: 0.7745 (pp30) REVERT: J 51 TYR cc_start: 0.8964 (p90) cc_final: 0.8725 (p90) REVERT: J 87 ASP cc_start: 0.8848 (m-30) cc_final: 0.8542 (m-30) REVERT: J 96 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8330 (mtm-85) REVERT: J 98 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: A 56 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8253 (mmtm) REVERT: A 114 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8733 (mtpp) REVERT: B 523 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 548 MET cc_start: 0.8769 (ttm) cc_final: 0.8463 (ttm) REVERT: B 551 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7504 (pp30) REVERT: C 54 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7323 (ttm170) REVERT: C 80 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6691 (p90) REVERT: C 213 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (mm) REVERT: D 25 SER cc_start: 0.8773 (m) cc_final: 0.8266 (p) REVERT: D 46 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 80 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8755 (mtpm) REVERT: D 87 ASN cc_start: 0.8900 (t0) cc_final: 0.8620 (t0) REVERT: D 110 ASP cc_start: 0.7601 (m-30) cc_final: 0.7209 (m-30) REVERT: E 85 GLU cc_start: 0.8139 (tt0) cc_final: 0.7931 (tt0) REVERT: E 87 ASP cc_start: 0.8762 (m-30) cc_final: 0.8388 (m-30) REVERT: E 94 ASP cc_start: 0.8151 (t0) cc_final: 0.7888 (t70) REVERT: E 98 ARG cc_start: 0.8535 (mpp80) cc_final: 0.8308 (mpp80) REVERT: E 108 LYS cc_start: 0.8817 (tptm) cc_final: 0.8494 (tptp) REVERT: K 184 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (pp) REVERT: L 523 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7162 (tm-30) REVERT: L 545 GLU cc_start: 0.8533 (mp0) cc_final: 0.8236 (mp0) REVERT: M 11 LEU cc_start: 0.8761 (tp) cc_final: 0.8483 (tp) REVERT: M 59 ASP cc_start: 0.8396 (t0) cc_final: 0.8044 (t0) REVERT: N 6 GLU cc_start: 0.7986 (mp0) cc_final: 0.7701 (mp0) REVERT: N 28 THR cc_start: 0.8683 (m) cc_final: 0.8377 (t) REVERT: N 46 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7437 (tm-30) REVERT: N 87 ASN cc_start: 0.8871 (t0) cc_final: 0.8637 (t0) REVERT: N 95 MET cc_start: 0.8534 (mtp) cc_final: 0.7794 (ttm) REVERT: O 44 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8711 (p) REVERT: O 85 GLU cc_start: 0.8339 (tt0) cc_final: 0.8090 (tt0) REVERT: O 87 ASP cc_start: 0.8800 (m-30) cc_final: 0.8518 (m-30) REVERT: O 108 LYS cc_start: 0.8766 (tptm) cc_final: 0.8420 (tptp) outliers start: 56 outliers final: 22 residues processed: 338 average time/residue: 0.6843 time to fit residues: 255.1256 Evaluate side-chains 314 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 30 SER 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 551 GLN Chi-restraints excluded: chain C residue 12 VAL 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 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 34 ASP 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 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: 5.9990 chunk 94 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058169 restraints weight = 46299.773| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.26 r_work: 0.2932 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17433 Z= 0.207 Angle : 0.623 11.712 23718 Z= 0.313 Chirality : 0.043 0.159 2634 Planarity : 0.004 0.038 3000 Dihedral : 4.317 59.862 2364 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.70 % Allowed : 17.48 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2127 helix: 1.10 (0.42), residues: 156 sheet: 0.01 (0.19), residues: 762 loop : -0.11 (0.18), residues: 1209 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 0.010 0.001 PHE N 70 TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (17391) covalent geometry : angle 0.61432 / 0.31 (23613) SS BOND : bond 0.00342 / 0.19 ( 21) SS BOND : angle 0.50415 / 0.29 ( 42) hydrogen bonds : bond 0.03642 / 2.46 ( 516) hydrogen bonds : angle 5.44904 / 3.87 ( 1410) link_ALPHA1-3 : bond 0.00196 / 0.10 ( 6) link_ALPHA1-3 : angle 1.69100 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00073 / 0.03 ( 3) link_ALPHA1-6 : angle 2.64461 / 1.42 ( 9) link_BETA1-4 : bond 0.00196 / 0.12 ( 6) link_BETA1-4 : angle 1.94890 / 1.17 ( 18) link_NAG-ASN : bond 0.00343 / 0.18 ( 6) link_NAG-ASN : angle 2.18661 / 1.41 ( 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 364 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8603 (mt0) cc_final: 0.7936 (mm-40) REVERT: F 54 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7966 (ptm160) REVERT: F 56 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8228 (mmtm) REVERT: F 127 ASP cc_start: 0.8394 (p0) cc_final: 0.7960 (p0) REVERT: G 523 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7362 (tm-30) REVERT: G 551 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: H 59 ASP cc_start: 0.8369 (t0) cc_final: 0.7902 (t0) REVERT: H 90 ASP cc_start: 0.6633 (m-30) cc_final: 0.6387 (m-30) REVERT: I 6 GLU cc_start: 0.8183 (mp0) cc_final: 0.7664 (mp0) REVERT: I 43 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8134 (tttm) REVERT: I 46 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: I 87 ASN cc_start: 0.8851 (t0) cc_final: 0.8590 (t0) REVERT: I 95 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: I 114 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7381 (mtm110) REVERT: J 16 GLN cc_start: 0.8067 (pt0) cc_final: 0.7854 (pp30) REVERT: J 41 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8351 (mm) REVERT: J 51 TYR cc_start: 0.9006 (p90) cc_final: 0.8762 (p90) REVERT: J 81 GLN cc_start: 0.8911 (mp10) cc_final: 0.8543 (mp10) REVERT: J 87 ASP cc_start: 0.8845 (m-30) cc_final: 0.8526 (m-30) REVERT: J 96 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8375 (mtm-85) REVERT: A 56 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8251 (mmtm) REVERT: A 114 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8716 (mtpp) REVERT: B 523 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7124 (tm-30) REVERT: B 551 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7506 (pp30) REVERT: C 13 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8693 (mmmm) REVERT: C 54 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7244 (ttm170) REVERT: C 59 ASP cc_start: 0.8360 (t0) cc_final: 0.8110 (t0) REVERT: C 213 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (mm) REVERT: D 3 GLN cc_start: 0.7981 (pp30) cc_final: 0.7748 (pp30) REVERT: D 25 SER cc_start: 0.8766 (m) cc_final: 0.8275 (p) REVERT: D 43 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8154 (mmmm) REVERT: D 46 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: D 80 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8688 (mtpm) REVERT: D 87 ASN cc_start: 0.9045 (t0) cc_final: 0.8823 (t0) REVERT: D 110 ASP cc_start: 0.7745 (m-30) cc_final: 0.7515 (m-30) REVERT: E 85 GLU cc_start: 0.8244 (tt0) cc_final: 0.7984 (tt0) REVERT: E 87 ASP cc_start: 0.8746 (m-30) cc_final: 0.8416 (m-30) REVERT: E 94 ASP cc_start: 0.8140 (t0) cc_final: 0.7813 (t70) REVERT: E 98 ARG cc_start: 0.8597 (mpp80) cc_final: 0.8308 (mpp80) REVERT: E 108 LYS cc_start: 0.8857 (tptm) cc_final: 0.8427 (tptt) REVERT: K 184 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8679 (pp) REVERT: L 523 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7273 (tm-30) REVERT: M 11 LEU cc_start: 0.8818 (tp) cc_final: 0.8604 (tp) REVERT: M 41 PRO cc_start: 0.8535 (Cg_exo) cc_final: 0.8259 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8375 (t0) cc_final: 0.7994 (t0) REVERT: M 156 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8121 (ttp80) REVERT: N 6 GLU cc_start: 0.8046 (mp0) cc_final: 0.7697 (mp0) REVERT: N 28 THR cc_start: 0.8689 (m) cc_final: 0.8380 (t) REVERT: N 43 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8400 (mmmm) REVERT: N 46 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7556 (tm-30) REVERT: N 87 ASN cc_start: 0.8941 (t0) cc_final: 0.8692 (t0) REVERT: N 95 MET cc_start: 0.8592 (mtp) cc_final: 0.7787 (ttm) REVERT: O 81 GLN cc_start: 0.8946 (mp10) cc_final: 0.8646 (mp10) REVERT: O 85 GLU cc_start: 0.8375 (tt0) cc_final: 0.8055 (tt0) REVERT: O 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8603 (m-30) REVERT: O 94 ASP cc_start: 0.8169 (t70) cc_final: 0.7671 (t70) REVERT: O 96 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8574 (mtm-85) REVERT: O 108 LYS cc_start: 0.8808 (tptm) cc_final: 0.8419 (tptp) outliers start: 66 outliers final: 34 residues processed: 330 average time/residue: 0.7201 time to fit residues: 260.8867 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 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 12 VAL 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 72 MET Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 34 ASP 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 232 THR Chi-restraints excluded: chain N residue 2 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 136 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.076872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058143 restraints weight = 46241.609| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.24 r_work: 0.2936 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17433 Z= 0.195 Angle : 0.625 8.998 23718 Z= 0.314 Chirality : 0.042 0.163 2634 Planarity : 0.004 0.033 3000 Dihedral : 4.336 59.770 2364 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.92 % Allowed : 17.87 % 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 are not related in a simple way. whole: -0.19 (0.18), residues: 2127 helix: 1.20 (0.42), residues: 156 sheet: -0.11 (0.19), residues: 759 loop : -0.23 (0.18), residues: 1212 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 I 70 TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (17391) covalent geometry : angle 0.61779 / 0.31 (23613) SS BOND : bond 0.00275 / 0.16 ( 21) SS BOND : angle 0.37853 / 0.21 ( 42) hydrogen bonds : bond 0.03424 / 2.32 ( 516) hydrogen bonds : angle 5.32575 / 3.78 ( 1410) link_ALPHA1-3 : bond 0.00237 / 0.13 ( 6) link_ALPHA1-3 : angle 1.59401 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00143 / 0.06 ( 3) link_ALPHA1-6 : angle 2.47427 / 1.33 ( 9) link_BETA1-4 : bond 0.00238 / 0.14 ( 6) link_BETA1-4 : angle 1.88325 / 1.10 ( 18) link_NAG-ASN : bond 0.00313 / 0.16 ( 6) link_NAG-ASN : angle 2.17658 / 1.39 ( 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 365 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 295 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8600 (mt0) cc_final: 0.8028 (mm-40) REVERT: F 54 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7986 (ptm160) REVERT: F 56 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8229 (mmtm) REVERT: F 100 GLU cc_start: 0.8764 (mp0) cc_final: 0.8506 (mp0) REVERT: F 127 ASP cc_start: 0.8385 (p0) cc_final: 0.7938 (p0) REVERT: G 523 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7171 (tm-30) REVERT: G 551 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7454 (pp30) REVERT: H 41 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8007 (Cg_endo) REVERT: H 59 ASP cc_start: 0.8218 (t0) cc_final: 0.7853 (t0) REVERT: H 156 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8299 (ttp80) REVERT: I 6 GLU cc_start: 0.8115 (mp0) cc_final: 0.7722 (mp0) REVERT: I 46 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: I 87 ASN cc_start: 0.8849 (t0) cc_final: 0.8588 (t0) REVERT: I 95 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7506 (ttm) REVERT: I 114 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7561 (mtm110) REVERT: J 16 GLN cc_start: 0.8017 (pt0) cc_final: 0.7765 (pp30) REVERT: J 26 TYR cc_start: 0.9455 (p90) cc_final: 0.9096 (p90) REVERT: J 51 TYR cc_start: 0.8988 (p90) cc_final: 0.8767 (p90) REVERT: J 68 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8396 (tmmm) REVERT: J 87 ASP cc_start: 0.8854 (m-30) cc_final: 0.8534 (m-30) REVERT: J 96 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8340 (mtm-85) REVERT: A 56 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8238 (mmtm) REVERT: A 114 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8711 (mtpp) REVERT: B 523 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 551 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: C 13 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8708 (mmmm) REVERT: C 54 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7246 (ttm170) REVERT: C 213 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 25 SER cc_start: 0.8789 (m) cc_final: 0.8203 (p) REVERT: D 46 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: D 67 ARG cc_start: 0.8059 (pmt-80) cc_final: 0.6581 (tpp80) REVERT: D 87 ASN cc_start: 0.9008 (t0) cc_final: 0.8779 (t0) REVERT: D 95 MET cc_start: 0.8282 (mtp) cc_final: 0.7522 (ttm) REVERT: E 81 GLN cc_start: 0.8733 (mp10) cc_final: 0.8199 (mp10) REVERT: E 85 GLU cc_start: 0.8216 (tt0) cc_final: 0.7954 (tt0) REVERT: E 87 ASP cc_start: 0.8764 (m-30) cc_final: 0.8370 (m-30) REVERT: E 94 ASP cc_start: 0.8085 (t0) cc_final: 0.7803 (t70) REVERT: E 96 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8575 (mtm-85) REVERT: E 98 ARG cc_start: 0.8637 (mpp80) cc_final: 0.8278 (mpp80) REVERT: E 108 LYS cc_start: 0.8854 (tptm) cc_final: 0.8506 (tptp) REVERT: K 77 THR cc_start: 0.8843 (p) cc_final: 0.8601 (t) REVERT: K 184 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (pp) REVERT: L 523 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7288 (tm-30) REVERT: M 11 LEU cc_start: 0.8862 (tp) cc_final: 0.8611 (tp) REVERT: M 59 ASP cc_start: 0.8333 (t0) cc_final: 0.8007 (t0) REVERT: M 89 GLU cc_start: 0.7996 (pp20) cc_final: 0.7649 (pp20) REVERT: M 156 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8284 (ttp80) REVERT: N 6 GLU cc_start: 0.8027 (mp0) cc_final: 0.7704 (mp0) REVERT: N 13 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8490 (mm110) REVERT: N 46 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7570 (tm-30) REVERT: N 87 ASN cc_start: 0.8939 (t0) cc_final: 0.8716 (t0) REVERT: N 95 MET cc_start: 0.8607 (mtp) cc_final: 0.7745 (ttm) REVERT: O 81 GLN cc_start: 0.8950 (mp10) cc_final: 0.8589 (mp10) REVERT: O 87 ASP cc_start: 0.8894 (m-30) cc_final: 0.8632 (m-30) REVERT: O 94 ASP cc_start: 0.8154 (t70) cc_final: 0.7670 (t70) REVERT: O 96 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8553 (mtm-85) REVERT: O 108 LYS cc_start: 0.8803 (tptm) cc_final: 0.8454 (tptp) outliers start: 70 outliers final: 37 residues processed: 334 average time/residue: 0.6928 time to fit residues: 254.8411 Evaluate side-chains 327 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 91 SER 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 5 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 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 88 LEU 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 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: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 GLN N 86 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.077385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057747 restraints weight = 45590.277| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.32 r_work: 0.2913 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17433 Z= 0.213 Angle : 0.638 8.279 23718 Z= 0.322 Chirality : 0.043 0.156 2634 Planarity : 0.004 0.047 3000 Dihedral : 4.381 59.696 2364 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.70 % Allowed : 18.94 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2127 helix: 1.29 (0.42), residues: 156 sheet: -0.19 (0.18), residues: 762 loop : -0.24 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 219 TYR 0.028 0.001 TYR E 51 PHE 0.014 0.001 PHE N 70 TRP 0.010 0.001 TRP D 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17391) covalent geometry : angle 0.63092 / 0.32 (23613) SS BOND : bond 0.00304 / 0.17 ( 21) SS BOND : angle 0.40554 / 0.23 ( 42) hydrogen bonds : bond 0.03383 / 2.29 ( 516) hydrogen bonds : angle 5.28891 / 3.75 ( 1410) link_ALPHA1-3 : bond 0.00207 / 0.12 ( 6) link_ALPHA1-3 : angle 1.64783 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00124 / 0.05 ( 3) link_ALPHA1-6 : angle 2.57180 / 1.38 ( 9) link_BETA1-4 : bond 0.00214 / 0.12 ( 6) link_BETA1-4 : angle 1.89358 / 1.11 ( 18) link_NAG-ASN : bond 0.00339 / 0.17 ( 6) link_NAG-ASN : angle 2.21438 / 1.41 ( 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 368 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 302 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8610 (mt0) cc_final: 0.8070 (mm-40) REVERT: F 54 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8009 (ptm160) REVERT: F 56 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8168 (mmtm) REVERT: F 100 GLU cc_start: 0.8716 (mp0) cc_final: 0.8497 (mp0) REVERT: F 127 ASP cc_start: 0.8456 (p0) cc_final: 0.8021 (p0) REVERT: G 523 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7134 (tm-30) REVERT: H 59 ASP cc_start: 0.8209 (t0) cc_final: 0.7883 (t0) REVERT: H 89 GLU cc_start: 0.8225 (pp20) cc_final: 0.7959 (pp20) REVERT: H 90 ASP cc_start: 0.6829 (m-30) cc_final: 0.6612 (m-30) REVERT: H 146 HIS cc_start: 0.7408 (m90) cc_final: 0.7155 (m90) REVERT: I 6 GLU cc_start: 0.8096 (mp0) cc_final: 0.7588 (mp0) REVERT: I 46 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: I 87 ASN cc_start: 0.8850 (t0) cc_final: 0.8583 (t0) REVERT: I 95 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7481 (ttm) REVERT: I 114 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7610 (mtm110) REVERT: J 51 TYR cc_start: 0.8982 (p90) cc_final: 0.8772 (p90) REVERT: J 68 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8327 (tmmm) REVERT: J 87 ASP cc_start: 0.8860 (m-30) cc_final: 0.8531 (m-30) REVERT: J 96 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8341 (mtm-85) REVERT: A 56 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8223 (mmtm) REVERT: A 114 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: B 523 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 551 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7395 (pp30) REVERT: C 13 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8740 (mmmm) REVERT: C 41 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8403 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8350 (pt0) REVERT: C 54 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7623 (ttp-170) REVERT: C 59 ASP cc_start: 0.8362 (t0) cc_final: 0.8130 (t0) REVERT: C 213 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 25 SER cc_start: 0.8766 (m) cc_final: 0.8304 (p) REVERT: D 46 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 67 ARG cc_start: 0.8142 (pmt-80) cc_final: 0.6621 (tpp80) REVERT: D 87 ASN cc_start: 0.8960 (t0) cc_final: 0.8710 (t0) REVERT: D 95 MET cc_start: 0.8273 (mtp) cc_final: 0.7485 (ttm) REVERT: E 81 GLN cc_start: 0.8857 (mp10) cc_final: 0.8411 (mp10) REVERT: E 85 GLU cc_start: 0.8275 (tt0) cc_final: 0.8038 (tt0) REVERT: E 87 ASP cc_start: 0.8782 (m-30) cc_final: 0.8349 (m-30) REVERT: E 94 ASP cc_start: 0.8165 (t0) cc_final: 0.7881 (t70) REVERT: E 96 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8585 (mtm-85) REVERT: E 98 ARG cc_start: 0.8584 (mpp80) cc_final: 0.8216 (mpp80) REVERT: E 108 LYS cc_start: 0.8846 (tptm) cc_final: 0.8522 (tptp) REVERT: E 109 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (tp) REVERT: K 77 THR cc_start: 0.8846 (p) cc_final: 0.8589 (t) REVERT: K 184 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8692 (pp) REVERT: L 522 ASP cc_start: 0.7550 (t70) cc_final: 0.7158 (t0) REVERT: M 11 LEU cc_start: 0.8840 (tp) cc_final: 0.8620 (tp) REVERT: M 54 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7175 (ttm170) REVERT: M 59 ASP cc_start: 0.8298 (t0) cc_final: 0.7963 (t0) REVERT: N 6 GLU cc_start: 0.7976 (mp0) cc_final: 0.7620 (mp0) REVERT: N 46 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7534 (tm-30) REVERT: N 61 ASP cc_start: 0.7801 (t0) cc_final: 0.7364 (t0) REVERT: N 87 ASN cc_start: 0.8934 (t0) cc_final: 0.8688 (t0) REVERT: N 95 MET cc_start: 0.8607 (mtp) cc_final: 0.7642 (ttm) REVERT: N 114 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7713 (mtm110) REVERT: O 81 GLN cc_start: 0.8923 (mp10) cc_final: 0.8503 (mp10) REVERT: O 85 GLU cc_start: 0.8343 (tt0) cc_final: 0.8081 (tt0) REVERT: O 94 ASP cc_start: 0.8181 (t70) cc_final: 0.7690 (t70) REVERT: O 96 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8551 (mtm-85) REVERT: O 108 LYS cc_start: 0.8781 (tptm) cc_final: 0.8408 (tptp) outliers start: 66 outliers final: 37 residues processed: 339 average time/residue: 0.6876 time to fit residues: 257.0305 Evaluate side-chains 330 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 91 SER 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 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 88 LEU 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 E residue 109 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 199 optimal weight: 0.0170 chunk 163 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 90 optimal weight: 0.0470 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN L 551 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059827 restraints weight = 45623.514| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.24 r_work: 0.2984 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17433 Z= 0.126 Angle : 0.634 9.976 23718 Z= 0.317 Chirality : 0.042 0.166 2634 Planarity : 0.004 0.041 3000 Dihedral : 4.241 57.795 2364 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.03 % Allowed : 20.78 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2127 helix: 1.42 (0.43), residues: 156 sheet: 0.14 (0.19), residues: 693 loop : -0.38 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 156 TYR 0.029 0.001 TYR E 51 PHE 0.007 0.001 PHE C 148 TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17391) covalent geometry : angle 0.62882 / 0.32 (23613) SS BOND : bond 0.00178 / 0.12 ( 21) SS BOND : angle 0.31752 / 0.19 ( 42) hydrogen bonds : bond 0.02982 / 2.01 ( 516) hydrogen bonds : angle 5.11336 / 3.61 ( 1410) link_ALPHA1-3 : bond 0.00510 / 0.28 ( 6) link_ALPHA1-3 : angle 1.41601 / 0.92 ( 18) link_ALPHA1-6 : bond 0.00573 / 0.26 ( 3) link_ALPHA1-6 : angle 2.03090 / 1.10 ( 9) link_BETA1-4 : bond 0.00510 / 0.29 ( 6) link_BETA1-4 : angle 1.72641 / 1.00 ( 18) link_NAG-ASN : bond 0.00090 / 0.05 ( 6) link_NAG-ASN : angle 1.89688 / 1.21 ( 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 363 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8610 (mt0) cc_final: 0.8091 (mm-40) REVERT: F 56 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8207 (mmtm) REVERT: F 100 GLU cc_start: 0.8756 (mp0) cc_final: 0.8555 (mp0) REVERT: F 127 ASP cc_start: 0.8338 (p0) cc_final: 0.7896 (p0) REVERT: G 523 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7348 (tm-30) REVERT: H 59 ASP cc_start: 0.8126 (t0) cc_final: 0.7850 (t0) REVERT: H 90 ASP cc_start: 0.6762 (m-30) cc_final: 0.6486 (m-30) REVERT: I 6 GLU cc_start: 0.7947 (mp0) cc_final: 0.7428 (mp0) REVERT: I 46 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: I 87 ASN cc_start: 0.8851 (t0) cc_final: 0.8632 (t0) REVERT: I 95 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7641 (ttm) REVERT: I 114 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7484 (mtm110) REVERT: J 87 ASP cc_start: 0.8861 (m-30) cc_final: 0.8540 (m-30) REVERT: J 94 ASP cc_start: 0.8001 (t0) cc_final: 0.7706 (t70) REVERT: A 56 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8229 (mmtm) REVERT: B 523 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 551 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7415 (pp30) REVERT: C 13 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8732 (mmmm) REVERT: C 34 MET cc_start: 0.9428 (mmm) cc_final: 0.9212 (tpt) REVERT: C 40 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7638 (tpp80) REVERT: C 41 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.7271 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7973 (mm110) REVERT: C 46 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8484 (pt0) REVERT: C 54 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.6693 (tpp80) REVERT: C 59 ASP cc_start: 0.8343 (t0) cc_final: 0.8093 (t0) REVERT: C 89 GLU cc_start: 0.8268 (pp20) cc_final: 0.7960 (pp20) REVERT: C 213 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 25 SER cc_start: 0.8761 (m) cc_final: 0.8318 (p) REVERT: D 39 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 46 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: D 67 ARG cc_start: 0.8071 (pmt-80) cc_final: 0.6669 (tpp80) REVERT: D 78 LYS cc_start: 0.9273 (mtmm) cc_final: 0.9004 (pmtt) REVERT: D 87 ASN cc_start: 0.9015 (t0) cc_final: 0.8810 (t0) REVERT: D 95 MET cc_start: 0.8297 (mtp) cc_final: 0.7583 (ttm) REVERT: E 68 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8133 (tmmm) REVERT: E 81 GLN cc_start: 0.8916 (mp10) cc_final: 0.8455 (mp10) REVERT: E 85 GLU cc_start: 0.8287 (tt0) cc_final: 0.8069 (tt0) REVERT: E 87 ASP cc_start: 0.8794 (m-30) cc_final: 0.8368 (m-30) REVERT: E 94 ASP cc_start: 0.8123 (t0) cc_final: 0.7885 (t70) REVERT: E 98 ARG cc_start: 0.8522 (mpp80) cc_final: 0.8132 (mpp80) REVERT: E 108 LYS cc_start: 0.8870 (tptm) cc_final: 0.8542 (tptp) REVERT: E 109 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (tp) REVERT: K 44 GLN cc_start: 0.8373 (mt0) cc_final: 0.7772 (mm-40) REVERT: K 77 THR cc_start: 0.8752 (p) cc_final: 0.8531 (t) REVERT: K 184 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (pp) REVERT: K 231 GLU cc_start: 0.6447 (mp0) cc_final: 0.6076 (mp0) REVERT: L 523 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7343 (tm-30) REVERT: L 551 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7485 (pp30) REVERT: M 11 LEU cc_start: 0.8898 (tp) cc_final: 0.8651 (tp) REVERT: M 43 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8214 (mm110) REVERT: M 54 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7298 (ttm110) REVERT: M 59 ASP cc_start: 0.8196 (t0) cc_final: 0.7903 (t0) REVERT: M 156 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8052 (ttp80) REVERT: N 39 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8442 (tm-30) REVERT: N 46 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7524 (tm-30) REVERT: N 61 ASP cc_start: 0.7763 (t0) cc_final: 0.7310 (t0) REVERT: N 95 MET cc_start: 0.8639 (mtp) cc_final: 0.7754 (ttm) REVERT: O 81 GLN cc_start: 0.8885 (mp10) cc_final: 0.8546 (mp10) REVERT: O 85 GLU cc_start: 0.8386 (tt0) cc_final: 0.8067 (tt0) REVERT: O 94 ASP cc_start: 0.8034 (t70) cc_final: 0.7564 (t70) REVERT: O 108 LYS cc_start: 0.8760 (tptm) cc_final: 0.8444 (tptt) outliers start: 54 outliers final: 32 residues processed: 344 average time/residue: 0.6910 time to fit residues: 261.8987 Evaluate side-chains 326 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER 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 88 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain A residue 78 ASP 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 D residue 88 LEU 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 E residue 109 LEU 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 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 16 GLN J 28 ASN J 100 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN O 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059108 restraints weight = 45972.723| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.24 r_work: 0.2961 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17433 Z= 0.157 Angle : 0.647 8.920 23718 Z= 0.325 Chirality : 0.042 0.174 2634 Planarity : 0.004 0.045 3000 Dihedral : 4.226 56.677 2364 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.97 % Allowed : 21.34 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2127 helix: 1.44 (0.43), residues: 156 sheet: 0.05 (0.19), residues: 714 loop : -0.34 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 219 TYR 0.028 0.001 TYR E 51 PHE 0.013 0.001 PHE N 70 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (17391) covalent geometry : angle 0.64077 / 0.32 (23613) SS BOND : bond 0.00190 / 0.11 ( 21) SS BOND : angle 0.58299 / 0.31 ( 42) hydrogen bonds : bond 0.03055 / 2.08 ( 516) hydrogen bonds : angle 5.02400 / 3.55 ( 1410) link_ALPHA1-3 : bond 0.00356 / 0.20 ( 6) link_ALPHA1-3 : angle 1.52539 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00352 / 0.16 ( 3) link_ALPHA1-6 : angle 2.22012 / 1.20 ( 9) link_BETA1-4 : bond 0.00413 / 0.23 ( 6) link_BETA1-4 : angle 1.88820 / 1.01 ( 18) link_NAG-ASN : bond 0.00107 / 0.05 ( 6) link_NAG-ASN : angle 1.91238 / 1.21 ( 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 342 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8604 (mt0) cc_final: 0.8082 (mm-40) REVERT: F 56 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8175 (mmtm) REVERT: F 127 ASP cc_start: 0.8357 (p0) cc_final: 0.7934 (p0) REVERT: G 523 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7334 (tm-30) REVERT: G 540 GLU cc_start: 0.8630 (pm20) cc_final: 0.8360 (mp0) REVERT: H 59 ASP cc_start: 0.8152 (t0) cc_final: 0.7867 (t0) REVERT: H 80 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: H 146 HIS cc_start: 0.7401 (m90) cc_final: 0.7145 (m90) REVERT: H 156 ARG cc_start: 0.8865 (tmt90) cc_final: 0.8550 (ttp80) REVERT: I 6 GLU cc_start: 0.7919 (mp0) cc_final: 0.7411 (mp0) REVERT: I 11 LEU cc_start: 0.8855 (tp) cc_final: 0.8522 (tm) REVERT: I 43 LYS cc_start: 0.8616 (ttmm) cc_final: 0.7826 (tttm) REVERT: I 46 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: I 87 ASN cc_start: 0.8837 (t0) cc_final: 0.8612 (t0) REVERT: I 95 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: I 114 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7480 (mtm110) REVERT: J 87 ASP cc_start: 0.8864 (m-30) cc_final: 0.8513 (m-30) REVERT: J 94 ASP cc_start: 0.8058 (t0) cc_final: 0.7790 (t70) REVERT: J 96 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8306 (mtm-85) REVERT: A 56 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8207 (mmtm) REVERT: A 114 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8632 (mtpp) REVERT: B 523 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 551 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7392 (pp30) REVERT: C 13 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8735 (mmmm) REVERT: C 34 MET cc_start: 0.9426 (mmm) cc_final: 0.9206 (tpt) REVERT: C 41 PRO cc_start: 0.8646 (Cg_exo) cc_final: 0.8433 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8501 (pt0) REVERT: C 54 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.6702 (tpp80) REVERT: C 89 GLU cc_start: 0.8221 (pp20) cc_final: 0.7886 (pp20) REVERT: C 213 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8557 (mm) REVERT: D 25 SER cc_start: 0.8827 (m) cc_final: 0.8301 (p) REVERT: D 39 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 46 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: D 67 ARG cc_start: 0.8083 (pmt-80) cc_final: 0.6626 (tpp80) REVERT: D 75 ASP cc_start: 0.8751 (t0) cc_final: 0.8537 (t0) REVERT: D 78 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8961 (mppt) REVERT: D 95 MET cc_start: 0.8317 (mtp) cc_final: 0.7538 (ttm) REVERT: D 114 ARG cc_start: 0.6932 (mpt180) cc_final: 0.6628 (mpt180) REVERT: E 81 GLN cc_start: 0.8914 (mp10) cc_final: 0.8439 (mp10) REVERT: E 85 GLU cc_start: 0.8291 (tt0) cc_final: 0.8072 (tt0) REVERT: E 87 ASP cc_start: 0.8793 (m-30) cc_final: 0.8368 (m-30) REVERT: E 94 ASP cc_start: 0.8180 (t0) cc_final: 0.7914 (t70) REVERT: E 98 ARG cc_start: 0.8534 (mpp80) cc_final: 0.8135 (mpp80) REVERT: E 108 LYS cc_start: 0.8897 (tptm) cc_final: 0.8584 (tptp) REVERT: E 109 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8470 (tp) REVERT: K 44 GLN cc_start: 0.8362 (mt0) cc_final: 0.7777 (mm-40) REVERT: K 77 THR cc_start: 0.8692 (p) cc_final: 0.8455 (t) REVERT: K 184 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8687 (pp) REVERT: K 231 GLU cc_start: 0.6499 (mp0) cc_final: 0.6117 (mp0) REVERT: M 43 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8227 (mm110) REVERT: M 59 ASP cc_start: 0.8217 (t0) cc_final: 0.7915 (t0) REVERT: M 156 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8074 (ttp80) REVERT: N 39 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 46 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: N 61 ASP cc_start: 0.7817 (t0) cc_final: 0.7359 (t0) REVERT: N 85 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: N 95 MET cc_start: 0.8627 (mtp) cc_final: 0.7722 (ttm) REVERT: O 81 GLN cc_start: 0.8900 (mp10) cc_final: 0.8558 (mp10) REVERT: O 85 GLU cc_start: 0.8394 (tt0) cc_final: 0.8065 (tt0) REVERT: O 94 ASP cc_start: 0.8075 (t70) cc_final: 0.7593 (t70) REVERT: O 108 LYS cc_start: 0.8780 (tptm) cc_final: 0.8455 (tptt) outliers start: 53 outliers final: 28 residues processed: 318 average time/residue: 0.7008 time to fit residues: 245.3998 Evaluate side-chains 319 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER 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 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 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 D residue 88 LEU 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 184 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR 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 46 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 0.0010 chunk 98 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.0980 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 188 GLN J 28 ASN A 188 GLN D 103 GLN E 28 ASN O 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.076743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057196 restraints weight = 45991.691| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.32 r_work: 0.2898 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17433 Z= 0.245 Angle : 0.706 8.928 23718 Z= 0.357 Chirality : 0.043 0.179 2634 Planarity : 0.005 0.043 3000 Dihedral : 4.382 56.345 2364 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.91 % Allowed : 21.79 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2127 helix: 1.50 (0.42), residues: 156 sheet: -0.36 (0.18), residues: 840 loop : -0.15 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 114 TYR 0.031 0.002 TYR J 51 PHE 0.020 0.001 PHE N 70 TRP 0.009 0.002 TRP D 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (17391) covalent geometry : angle 0.69843 / 0.36 (23613) SS BOND : bond 0.00321 / 0.18 ( 21) SS BOND : angle 0.50422 / 0.28 ( 42) hydrogen bonds : bond 0.03385 / 2.31 ( 516) hydrogen bonds : angle 5.16141 / 3.65 ( 1410) link_ALPHA1-3 : bond 0.00079 / 0.05 ( 6) link_ALPHA1-3 : angle 1.70072 / 1.10 ( 18) link_ALPHA1-6 : bond 0.00078 / 0.04 ( 3) link_ALPHA1-6 : angle 2.65809 / 1.42 ( 9) link_BETA1-4 : bond 0.00144 / 0.08 ( 6) link_BETA1-4 : angle 2.03649 / 1.15 ( 18) link_NAG-ASN : bond 0.00373 / 0.19 ( 6) link_NAG-ASN : angle 2.22731 / 1.39 ( 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 337 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8601 (mt0) cc_final: 0.8030 (mm-40) REVERT: F 54 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8047 (ptm-80) REVERT: F 56 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8170 (mmtm) REVERT: F 127 ASP cc_start: 0.8470 (p0) cc_final: 0.8060 (p0) REVERT: G 523 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7367 (tm-30) REVERT: H 59 ASP cc_start: 0.8263 (t0) cc_final: 0.7866 (t0) REVERT: H 80 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: H 146 HIS cc_start: 0.7507 (m90) cc_final: 0.7251 (m90) REVERT: H 156 ARG cc_start: 0.8865 (tmt90) cc_final: 0.8508 (ttp80) REVERT: I 6 GLU cc_start: 0.8063 (mp0) cc_final: 0.7653 (mp0) REVERT: I 11 LEU cc_start: 0.8845 (tp) cc_final: 0.8530 (tm) REVERT: I 46 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: I 87 ASN cc_start: 0.8862 (t0) cc_final: 0.8610 (t0) REVERT: I 95 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7514 (ttm) REVERT: I 114 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7596 (mtm110) REVERT: J 87 ASP cc_start: 0.8814 (m-30) cc_final: 0.8492 (m-30) REVERT: J 96 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8337 (mtm-85) REVERT: A 56 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8183 (mmtm) REVERT: A 77 THR cc_start: 0.8916 (p) cc_final: 0.8518 (t) REVERT: A 114 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: A 156 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 523 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 551 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7389 (pp30) REVERT: C 13 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8747 (mmmm) REVERT: C 41 PRO cc_start: 0.8687 (Cg_exo) cc_final: 0.8057 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8024 (mm110) REVERT: C 46 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8470 (pt0) REVERT: C 54 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.7440 (ttp-170) REVERT: C 59 ASP cc_start: 0.8467 (t0) cc_final: 0.8149 (t0) REVERT: C 139 ASP cc_start: 0.8685 (p0) cc_final: 0.8399 (p0) REVERT: C 213 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (mm) REVERT: D 25 SER cc_start: 0.8822 (m) cc_final: 0.8309 (p) REVERT: D 46 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: D 67 ARG cc_start: 0.8132 (pmt-80) cc_final: 0.6623 (tpp80) REVERT: D 95 MET cc_start: 0.8327 (mtp) cc_final: 0.7393 (ttm) REVERT: E 68 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8209 (tmmm) REVERT: E 81 GLN cc_start: 0.8825 (mp10) cc_final: 0.8364 (mp10) REVERT: E 85 GLU cc_start: 0.8285 (tt0) cc_final: 0.8039 (tt0) REVERT: E 94 ASP cc_start: 0.8234 (t0) cc_final: 0.7963 (t70) REVERT: E 98 ARG cc_start: 0.8596 (mpp80) cc_final: 0.8338 (mpp80) REVERT: E 108 LYS cc_start: 0.8869 (tptm) cc_final: 0.8533 (tptp) REVERT: K 44 GLN cc_start: 0.8365 (mt0) cc_final: 0.7804 (mm-40) REVERT: K 77 THR cc_start: 0.8862 (p) cc_final: 0.8634 (t) REVERT: K 184 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8739 (pp) REVERT: K 231 GLU cc_start: 0.6544 (mp0) cc_final: 0.6154 (mp0) REVERT: M 59 ASP cc_start: 0.8316 (t0) cc_final: 0.8000 (t0) REVERT: M 156 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8065 (ttp80) REVERT: N 39 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8393 (tm-30) REVERT: N 46 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: N 61 ASP cc_start: 0.7889 (t0) cc_final: 0.7383 (t0) REVERT: N 78 LYS cc_start: 0.9284 (mtmm) cc_final: 0.9028 (pmtt) REVERT: N 85 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: N 95 MET cc_start: 0.8590 (mtp) cc_final: 0.7542 (ttm) REVERT: O 81 GLN cc_start: 0.8845 (mp10) cc_final: 0.8421 (mp10) REVERT: O 85 GLU cc_start: 0.8351 (tt0) cc_final: 0.7958 (tt0) REVERT: O 94 ASP cc_start: 0.8232 (t70) cc_final: 0.7717 (t70) REVERT: O 108 LYS cc_start: 0.8770 (tptm) cc_final: 0.8411 (tptt) outliers start: 52 outliers final: 30 residues processed: 313 average time/residue: 0.6999 time to fit residues: 241.2825 Evaluate side-chains 318 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG 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 67 ARG 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 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 D residue 88 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 41 LEU 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 71 THR Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 85 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 143 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.0070 chunk 206 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 176 optimal weight: 0.0980 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 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 = 0.3534 r_free = 0.3534 target = 0.078216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058786 restraints weight = 45537.175| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.34 r_work: 0.2937 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17433 Z= 0.146 Angle : 0.693 9.551 23718 Z= 0.349 Chirality : 0.042 0.168 2634 Planarity : 0.005 0.063 3000 Dihedral : 4.183 56.046 2362 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.46 % Allowed : 22.69 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2127 helix: 1.50 (0.42), residues: 156 sheet: -0.10 (0.19), residues: 723 loop : -0.34 (0.18), residues: 1248 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 0.016 0.001 PHE N 70 TRP 0.011 0.001 TRP C 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17391) covalent geometry : angle 0.68753 / 0.35 (23613) SS BOND : bond 0.00175 / 0.10 ( 21) SS BOND : angle 0.36646 / 0.22 ( 42) hydrogen bonds : bond 0.03046 / 2.06 ( 516) hydrogen bonds : angle 5.12383 / 3.61 ( 1410) link_ALPHA1-3 : bond 0.00371 / 0.20 ( 6) link_ALPHA1-3 : angle 1.54945 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00412 / 0.19 ( 3) link_ALPHA1-6 : angle 2.17498 / 1.17 ( 9) link_BETA1-4 : bond 0.00457 / 0.26 ( 6) link_BETA1-4 : angle 1.96022 / 1.09 ( 18) link_NAG-ASN : bond 0.00125 / 0.06 ( 6) link_NAG-ASN : angle 2.03357 / 1.28 ( 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 328 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8572 (mt0) cc_final: 0.8033 (mm-40) REVERT: F 56 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8158 (mmtm) REVERT: F 127 ASP cc_start: 0.8409 (p0) cc_final: 0.7997 (p0) REVERT: G 523 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 59 ASP cc_start: 0.8217 (t0) cc_final: 0.7829 (t0) REVERT: H 80 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: H 146 HIS cc_start: 0.7450 (m90) cc_final: 0.7177 (m90) REVERT: H 156 ARG cc_start: 0.8864 (tmt90) cc_final: 0.8525 (ttp80) REVERT: I 6 GLU cc_start: 0.7961 (mp0) cc_final: 0.7557 (mp0) REVERT: I 11 LEU cc_start: 0.8839 (tp) cc_final: 0.8503 (tm) REVERT: I 43 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7740 (tttm) REVERT: I 46 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: I 87 ASN cc_start: 0.8818 (t0) cc_final: 0.8572 (t0) REVERT: I 95 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: I 114 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7475 (mtm110) REVERT: J 87 ASP cc_start: 0.8812 (m-30) cc_final: 0.8492 (m-30) REVERT: J 94 ASP cc_start: 0.8097 (t0) cc_final: 0.7843 (t70) REVERT: J 96 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8299 (mtm-85) REVERT: A 56 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8186 (mmtm) REVERT: A 114 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8627 (mtpp) REVERT: A 156 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 523 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 551 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: C 13 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8743 (mmmm) REVERT: C 34 MET cc_start: 0.9371 (mmm) cc_final: 0.9139 (tpt) REVERT: C 41 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.7503 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8034 (mm110) REVERT: C 46 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8503 (pt0) REVERT: C 54 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7418 (ttp-170) REVERT: C 59 ASP cc_start: 0.8488 (t0) cc_final: 0.8163 (t0) REVERT: C 213 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8574 (mm) REVERT: D 25 SER cc_start: 0.8842 (m) cc_final: 0.8307 (p) REVERT: D 39 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 46 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: D 67 ARG cc_start: 0.8138 (pmt-80) cc_final: 0.6661 (tpp80) REVERT: D 78 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9091 (pmtt) REVERT: D 95 MET cc_start: 0.8339 (mtp) cc_final: 0.7470 (ttm) REVERT: E 68 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8170 (tmmm) REVERT: E 81 GLN cc_start: 0.8828 (mp10) cc_final: 0.8373 (mp10) REVERT: E 85 GLU cc_start: 0.8272 (tt0) cc_final: 0.8020 (tt0) REVERT: E 94 ASP cc_start: 0.8178 (t0) cc_final: 0.7941 (t70) REVERT: E 98 ARG cc_start: 0.8536 (mpp80) cc_final: 0.8243 (mpp80) REVERT: E 108 LYS cc_start: 0.8855 (tptm) cc_final: 0.8557 (tptp) REVERT: E 109 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8416 (tp) REVERT: K 44 GLN cc_start: 0.8358 (mt0) cc_final: 0.7806 (mm-40) REVERT: K 184 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8679 (pp) REVERT: K 231 GLU cc_start: 0.6499 (mp0) cc_final: 0.6101 (mp0) REVERT: M 11 LEU cc_start: 0.8890 (tp) cc_final: 0.8671 (tt) REVERT: M 43 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8248 (mm110) REVERT: M 59 ASP cc_start: 0.8297 (t0) cc_final: 0.8014 (t0) REVERT: M 156 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8049 (ttp80) REVERT: N 39 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8319 (tm-30) REVERT: N 46 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: N 61 ASP cc_start: 0.7831 (t0) cc_final: 0.7322 (t0) REVERT: N 78 LYS cc_start: 0.9285 (mtmm) cc_final: 0.9053 (pmtt) REVERT: N 85 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: N 95 MET cc_start: 0.8595 (mtp) cc_final: 0.7540 (ttm) REVERT: O 81 GLN cc_start: 0.8883 (mp10) cc_final: 0.8472 (mp10) REVERT: O 85 GLU cc_start: 0.8381 (tt0) cc_final: 0.8077 (tt0) REVERT: O 94 ASP cc_start: 0.8171 (t70) cc_final: 0.7694 (t70) REVERT: O 108 LYS cc_start: 0.8763 (tptm) cc_final: 0.8429 (tptt) outliers start: 44 outliers final: 26 residues processed: 308 average time/residue: 0.6977 time to fit residues: 236.6540 Evaluate side-chains 315 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 67 ARG 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 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 D residue 88 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR 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 85 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: 0.1980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 151 optimal weight: 0.0370 chunk 201 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 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 = 0.3522 r_free = 0.3522 target = 0.077691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059135 restraints weight = 45612.738| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.24 r_work: 0.2963 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17433 Z= 0.143 Angle : 0.680 10.007 23718 Z= 0.343 Chirality : 0.042 0.163 2634 Planarity : 0.004 0.060 3000 Dihedral : 4.118 55.339 2362 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.52 % Allowed : 22.41 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2127 helix: 1.58 (0.42), residues: 156 sheet: -0.03 (0.19), residues: 717 loop : -0.35 (0.18), residues: 1254 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 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17391) covalent geometry : angle 0.67427 / 0.34 (23613) SS BOND : bond 0.00158 / 0.10 ( 21) SS BOND : angle 0.36331 / 0.22 ( 42) hydrogen bonds : bond 0.02975 / 2.02 ( 516) hydrogen bonds : angle 5.06161 / 3.56 ( 1410) link_ALPHA1-3 : bond 0.00397 / 0.21 ( 6) link_ALPHA1-3 : angle 1.50667 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00403 / 0.19 ( 3) link_ALPHA1-6 : angle 2.10325 / 1.13 ( 9) link_BETA1-4 : bond 0.00470 / 0.26 ( 6) link_BETA1-4 : angle 1.95593 / 1.08 ( 18) link_NAG-ASN : bond 0.00090 / 0.04 ( 6) link_NAG-ASN : angle 1.95103 / 1.23 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6166.02 seconds wall clock time: 106 minutes 16.99 seconds (6376.99 seconds total)