Starting phenix.real_space_refine on Wed May 21 14:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpm_27638/05_2025/8dpm_27638.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 1.37s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16992 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "K" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "L" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.41, per 1000 atoms: 0.61 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: 4.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.53 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: 6.34 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5454 1.34 - 1.46: 4069 1.46 - 1.58: 7775 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 17391 Sorted by residual: bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 MAN Q 4 " pdb=" C2 MAN Q 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 MAN P 6 " pdb=" C2 MAN P 6 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 MAN Q 6 " pdb=" C2 MAN Q 6 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 17386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 23051 1.30 - 2.61: 404 2.61 - 3.91: 101 3.91 - 5.21: 39 5.21 - 6.51: 18 Bond angle restraints: 23613 Sorted by residual: angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" N THR C 241 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.20e+00 angle pdb=" C GLN G 551 " pdb=" N ASP G 552 " pdb=" CA ASP G 552 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" C GLN L 551 " pdb=" N ASP L 552 " pdb=" CA ASP L 552 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.29e+00 angle pdb=" C GLN B 551 " pdb=" N ASP B 552 " pdb=" CA ASP B 552 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.16e+00 angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" O GLY C 240 " ideal model delta sigma weight residual 122.33 120.57 1.76 8.10e-01 1.52e+00 4.71e+00 ... (remaining 23608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10148 21.43 - 42.87: 213 42.87 - 64.30: 31 64.30 - 85.74: 27 85.74 - 107.17: 12 Dihedral angle restraints: 10431 sinusoidal: 4299 harmonic: 6132 Sorted by residual: dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.46 107.17 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.44 107.15 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.41 107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2372 0.072 - 0.144: 251 0.144 - 0.216: 2 0.216 - 0.288: 3 0.288 - 0.360: 6 Chirality restraints: 2634 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN L 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2631 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 234 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 233 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO M 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO M 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 234 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.94e+00 pdb=" N PRO H 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " -0.024 5.00e-02 4.00e+02 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2055 2.76 - 3.29: 16011 3.29 - 3.83: 28969 3.83 - 4.36: 35505 4.36 - 4.90: 62154 Nonbonded interactions: 144694 Sorted by model distance: nonbonded pdb=" OG SER F 65 " pdb=" OE1 GLU F 100 " model vdw 2.221 3.040 nonbonded pdb=" OG SER K 65 " pdb=" OE1 GLU K 100 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 65 " pdb=" OE1 GLU A 100 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 117 " pdb=" OG SER A 119 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR O 33 " pdb=" OD1 ASP O 99 " model vdw 2.271 3.040 ... (remaining 144689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'Q' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17433 Z= 0.123 Angle : 0.580 25.680 23718 Z= 0.271 Chirality : 0.044 0.360 2634 Planarity : 0.003 0.043 3000 Dihedral : 10.748 107.173 6486 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.62 % Allowed : 5.04 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.006 0.001 TRP C 33 HIS 0.001 0.000 HIS A 154 PHE 0.004 0.001 PHE L 582 TYR 0.014 0.001 TYR M 187 ARG 0.002 0.000 ARG F 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 6) link_NAG-ASN : angle 10.66703 ( 18) link_ALPHA1-6 : bond 0.00431 ( 3) link_ALPHA1-6 : angle 1.54262 ( 9) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 1.73258 ( 18) link_ALPHA1-3 : bond 0.00478 ( 6) link_ALPHA1-3 : angle 1.46144 ( 18) hydrogen bonds : bond 0.22436 ( 516) hydrogen bonds : angle 8.99463 ( 1410) SS BOND : bond 0.00103 ( 21) SS BOND : angle 0.57553 ( 42) covalent geometry : bond 0.00239 (17391) covalent geometry : angle 0.49548 (23613) *********************** 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 : 1.708 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: 0.7188 (p90) REVERT: C 90 ASP cc_start: 0.6511 (m-30) cc_final: 0.6260 (m-30) outliers start: 11 outliers final: 3 residues processed: 476 average time/residue: 1.3423 time to fit residues: 708.4661 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 : 1.739 ------------------------------------------------------------------------------- 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 177 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS 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 K 188 GLN L 521 GLN M 52 ASN N 103 GLN O 28 ASN O 100 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056224 restraints weight = 46403.912| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.32 r_work: 0.2872 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 17433 Z= 0.399 Angle : 0.766 8.376 23718 Z= 0.389 Chirality : 0.047 0.187 2634 Planarity : 0.005 0.052 3000 Dihedral : 8.373 73.410 2783 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.37 % Allowed : 16.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2127 helix: 0.31 (0.41), residues: 156 sheet: 0.01 (0.18), residues: 864 loop : -0.02 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 36 HIS 0.006 0.002 HIS M 35 PHE 0.020 0.002 PHE D 70 TYR 0.023 0.002 TYR E 51 ARG 0.008 0.001 ARG L 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 6) link_NAG-ASN : angle 2.97301 ( 18) link_ALPHA1-6 : bond 0.00809 ( 3) link_ALPHA1-6 : angle 3.11472 ( 9) link_BETA1-4 : bond 0.00278 ( 6) link_BETA1-4 : angle 2.89367 ( 18) link_ALPHA1-3 : bond 0.00156 ( 6) link_ALPHA1-3 : angle 2.53956 ( 18) hydrogen bonds : bond 0.05249 ( 516) hydrogen bonds : angle 6.12968 ( 1410) SS BOND : bond 0.00584 ( 21) SS BOND : angle 0.87029 ( 42) covalent geometry : bond 0.00892 (17391) covalent geometry : angle 0.75225 (23613) *********************** 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 385 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8568 (mt0) cc_final: 0.7938 (mm-40) REVERT: F 54 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (ptm160) REVERT: F 100 GLU cc_start: 0.8668 (mp0) cc_final: 0.8413 (mp0) REVERT: F 136 ARG cc_start: 0.8465 (tpt90) cc_final: 0.8013 (tmt-80) REVERT: G 523 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7143 (tm-30) REVERT: I 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7389 (mp0) REVERT: I 46 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 67 ARG cc_start: 0.6848 (tpp-160) cc_final: 0.6648 (tpp-160) REVERT: I 117 LEU cc_start: 0.9073 (tt) cc_final: 0.8844 (tm) REVERT: J 16 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: J 26 TYR cc_start: 0.9455 (p90) cc_final: 0.9138 (p90) REVERT: J 44 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8719 (p) REVERT: J 83 GLU cc_start: 0.8755 (pt0) cc_final: 0.8504 (pm20) REVERT: J 96 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8357 (mtm-85) REVERT: A 56 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8208 (mmtm) REVERT: A 114 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (mtpp) REVERT: B 523 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 551 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7422 (pp30) REVERT: C 80 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6891 (p90) REVERT: C 213 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8752 (mm) REVERT: D 25 SER cc_start: 0.8966 (m) cc_final: 0.8325 (p) REVERT: D 43 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8279 (mmmm) REVERT: D 46 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 75 ASP cc_start: 0.8732 (t0) cc_final: 0.8412 (p0) REVERT: D 80 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8722 (mtpm) REVERT: D 87 ASN cc_start: 0.8908 (t0) cc_final: 0.8697 (t0) REVERT: D 110 ASP cc_start: 0.7895 (m-30) cc_final: 0.7677 (m-30) REVERT: E 85 GLU cc_start: 0.8306 (tt0) cc_final: 0.8077 (tt0) REVERT: E 87 ASP cc_start: 0.8774 (m-30) cc_final: 0.8443 (m-30) REVERT: K 54 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7903 (ptm160) REVERT: L 523 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7299 (tm-30) REVERT: L 545 GLU cc_start: 0.8546 (mp0) cc_final: 0.8307 (mp0) REVERT: M 59 ASP cc_start: 0.8450 (t0) cc_final: 0.7997 (t0) REVERT: M 156 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8316 (ttp80) REVERT: N 28 THR cc_start: 0.8800 (m) cc_final: 0.8498 (t) REVERT: N 43 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8484 (mmmm) REVERT: N 46 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7533 (tm-30) REVERT: N 61 ASP cc_start: 0.8032 (t0) cc_final: 0.7741 (t0) REVERT: N 67 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6562 (tpp-160) REVERT: N 95 MET cc_start: 0.8531 (mtp) cc_final: 0.7646 (ttm) REVERT: O 16 GLN cc_start: 0.8380 (pt0) cc_final: 0.8121 (pp30) REVERT: O 44 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8654 (p) REVERT: O 85 GLU cc_start: 0.8431 (tt0) cc_final: 0.8093 (tt0) REVERT: O 108 LYS cc_start: 0.8774 (tptm) cc_final: 0.8374 (tptp) outliers start: 78 outliers final: 31 residues processed: 348 average time/residue: 1.3925 time to fit residues: 533.8630 Evaluate side-chains 311 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 80 PHE Chi-restraints excluded: chain H residue 91 SER 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 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 96 ARG 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 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 97 LEU 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 142 VAL 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 189 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 516 HIS J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058918 restraints weight = 45735.778| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.23 r_work: 0.2959 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17433 Z= 0.158 Angle : 0.622 7.786 23718 Z= 0.312 Chirality : 0.043 0.158 2634 Planarity : 0.004 0.033 3000 Dihedral : 7.768 65.623 2781 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.36 % Allowed : 17.93 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2127 helix: 0.73 (0.42), residues: 156 sheet: 0.14 (0.19), residues: 741 loop : -0.11 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE N 70 TYR 0.026 0.001 TYR J 51 ARG 0.008 0.001 ARG N 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 2.51883 ( 18) link_ALPHA1-6 : bond 0.00075 ( 3) link_ALPHA1-6 : angle 2.17980 ( 9) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 2.15763 ( 18) link_ALPHA1-3 : bond 0.00725 ( 6) link_ALPHA1-3 : angle 1.64144 ( 18) hydrogen bonds : bond 0.03834 ( 516) hydrogen bonds : angle 5.66632 ( 1410) SS BOND : bond 0.00286 ( 21) SS BOND : angle 0.48517 ( 42) covalent geometry : bond 0.00346 (17391) covalent geometry : angle 0.61352 (23613) *********************** 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 374 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8583 (mt0) cc_final: 0.7970 (mm-40) REVERT: F 100 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: F 127 ASP cc_start: 0.8288 (p0) cc_final: 0.7870 (p0) REVERT: G 523 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7267 (tm-30) REVERT: I 6 GLU cc_start: 0.8076 (mp0) cc_final: 0.7712 (mp0) REVERT: I 43 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8309 (tttm) REVERT: I 46 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: I 87 ASN cc_start: 0.8925 (t0) cc_final: 0.8702 (t0) REVERT: I 95 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: I 114 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7459 (mtm110) REVERT: I 117 LEU cc_start: 0.9116 (tt) cc_final: 0.8912 (tm) REVERT: J 51 TYR cc_start: 0.9014 (p90) cc_final: 0.8730 (p90) REVERT: J 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8563 (m-30) REVERT: A 56 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8255 (mmtm) REVERT: B 523 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 551 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (pp30) REVERT: C 34 MET cc_start: 0.9450 (mmm) cc_final: 0.9196 (tpt) REVERT: C 43 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7934 (mm110) REVERT: C 54 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7260 (ttm170) REVERT: C 80 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6750 (p90) REVERT: C 213 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 25 SER cc_start: 0.8760 (m) cc_final: 0.8334 (p) REVERT: D 43 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8261 (mmmm) REVERT: D 46 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 80 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8681 (mtpm) REVERT: D 87 ASN cc_start: 0.8918 (t0) cc_final: 0.8650 (t0) REVERT: E 85 GLU cc_start: 0.8236 (tt0) cc_final: 0.7944 (tt0) REVERT: E 87 ASP cc_start: 0.8748 (m-30) cc_final: 0.8356 (m-30) REVERT: E 94 ASP cc_start: 0.8182 (t0) cc_final: 0.7918 (t70) REVERT: E 108 LYS cc_start: 0.8815 (tptm) cc_final: 0.8491 (tptp) REVERT: K 54 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7634 (tpt90) REVERT: K 56 LYS cc_start: 0.8657 (mptt) cc_final: 0.8372 (mmtt) REVERT: K 120 GLU cc_start: 0.8418 (pm20) cc_final: 0.8163 (pm20) REVERT: L 523 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 545 GLU cc_start: 0.8532 (mp0) cc_final: 0.8256 (mp0) REVERT: M 59 ASP cc_start: 0.8415 (t0) cc_final: 0.8034 (t0) REVERT: M 156 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8328 (ttp80) REVERT: N 6 GLU cc_start: 0.8060 (mp0) cc_final: 0.7838 (mp0) REVERT: N 28 THR cc_start: 0.8735 (m) cc_final: 0.8406 (t) REVERT: N 43 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8408 (mmmm) REVERT: N 46 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7543 (tm-30) REVERT: N 87 ASN cc_start: 0.8825 (t0) cc_final: 0.8619 (t0) REVERT: N 95 MET cc_start: 0.8537 (mtp) cc_final: 0.7735 (ttm) REVERT: O 16 GLN cc_start: 0.8249 (pt0) cc_final: 0.7977 (pp30) REVERT: O 44 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8710 (p) REVERT: O 87 ASP cc_start: 0.8808 (m-30) cc_final: 0.8518 (m-30) REVERT: O 108 LYS cc_start: 0.8811 (tptm) cc_final: 0.8427 (tptp) outliers start: 60 outliers final: 24 residues processed: 340 average time/residue: 1.3235 time to fit residues: 497.9074 Evaluate side-chains 308 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU 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 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 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 106 ASP 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 E residue 34 ASP Chi-restraints excluded: chain K residue 54 ARG 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 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 59 ARG 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 143 optimal weight: 2.9990 chunk 171 optimal weight: 0.0470 chunk 66 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN J 100 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** 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 = 0.077423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058807 restraints weight = 45647.743| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.22 r_work: 0.2960 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17433 Z= 0.159 Angle : 0.613 10.750 23718 Z= 0.306 Chirality : 0.042 0.157 2634 Planarity : 0.004 0.046 3000 Dihedral : 7.518 61.257 2781 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.59 % Allowed : 18.54 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2127 helix: 1.00 (0.42), residues: 156 sheet: 0.09 (0.19), residues: 741 loop : -0.15 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE N 70 TYR 0.027 0.001 TYR E 51 ARG 0.010 0.001 ARG N 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.22518 ( 18) link_ALPHA1-6 : bond 0.00050 ( 3) link_ALPHA1-6 : angle 2.16500 ( 9) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 2.20358 ( 18) link_ALPHA1-3 : bond 0.00635 ( 6) link_ALPHA1-3 : angle 1.85108 ( 18) hydrogen bonds : bond 0.03503 ( 516) hydrogen bonds : angle 5.41098 ( 1410) SS BOND : bond 0.00244 ( 21) SS BOND : angle 0.39863 ( 42) covalent geometry : bond 0.00352 (17391) covalent geometry : angle 0.60397 (23613) *********************** 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 360 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8560 (mt0) cc_final: 0.7991 (mm-40) REVERT: F 56 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8183 (mmtm) REVERT: F 100 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: F 127 ASP cc_start: 0.8351 (p0) cc_final: 0.7920 (p0) REVERT: G 523 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7336 (tm-30) REVERT: H 90 ASP cc_start: 0.6679 (m-30) cc_final: 0.6453 (m-30) REVERT: I 6 GLU cc_start: 0.8079 (mp0) cc_final: 0.7636 (mp0) REVERT: I 43 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8206 (tttm) REVERT: I 46 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: I 85 MET cc_start: 0.8456 (mtt) cc_final: 0.8186 (mtt) REVERT: I 87 ASN cc_start: 0.8966 (t0) cc_final: 0.8704 (t0) REVERT: I 95 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7812 (ttm) REVERT: I 114 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7530 (mtm110) REVERT: I 117 LEU cc_start: 0.9145 (tt) cc_final: 0.8923 (tm) REVERT: J 16 GLN cc_start: 0.7987 (pt0) cc_final: 0.7647 (pt0) REVERT: J 51 TYR cc_start: 0.8966 (p90) cc_final: 0.8732 (p90) REVERT: J 87 ASP cc_start: 0.8873 (m-30) cc_final: 0.8550 (m-30) REVERT: J 94 ASP cc_start: 0.8072 (t0) cc_final: 0.7795 (t70) REVERT: J 96 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8415 (mtm-85) REVERT: J 98 ARG cc_start: 0.8529 (mtt90) cc_final: 0.8111 (mpp80) REVERT: A 56 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8244 (mmtm) REVERT: B 523 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 551 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: C 13 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8702 (mmmm) REVERT: C 54 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7254 (ttm170) REVERT: C 213 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8602 (mm) REVERT: D 25 SER cc_start: 0.8796 (m) cc_final: 0.8313 (p) REVERT: D 46 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: D 87 ASN cc_start: 0.8948 (t0) cc_final: 0.8694 (t0) REVERT: D 95 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7450 (ttm) REVERT: D 114 ARG cc_start: 0.7213 (mpt180) cc_final: 0.6919 (mpt180) REVERT: E 81 GLN cc_start: 0.8864 (mp10) cc_final: 0.8457 (mp10) REVERT: E 85 GLU cc_start: 0.8298 (tt0) cc_final: 0.8011 (tt0) REVERT: E 87 ASP cc_start: 0.8756 (m-30) cc_final: 0.8372 (m-30) REVERT: E 94 ASP cc_start: 0.8070 (t0) cc_final: 0.7816 (t70) REVERT: E 108 LYS cc_start: 0.8825 (tptm) cc_final: 0.8478 (tptp) REVERT: K 77 THR cc_start: 0.8840 (p) cc_final: 0.8586 (t) REVERT: L 523 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7239 (tm-30) REVERT: L 545 GLU cc_start: 0.8513 (mp0) cc_final: 0.8283 (mp0) REVERT: L 551 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7618 (pp30) REVERT: M 41 PRO cc_start: 0.8598 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8376 (t0) cc_final: 0.8016 (t0) REVERT: M 213 ILE cc_start: 0.8704 (mp) cc_final: 0.8408 (mm) REVERT: N 6 GLU cc_start: 0.8012 (mp0) cc_final: 0.7657 (mp0) REVERT: N 46 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7535 (tm-30) REVERT: N 87 ASN cc_start: 0.8874 (t0) cc_final: 0.8607 (t0) REVERT: N 95 MET cc_start: 0.8599 (mtp) cc_final: 0.7806 (ttm) REVERT: O 16 GLN cc_start: 0.8266 (pt0) cc_final: 0.8001 (pp30) REVERT: O 81 GLN cc_start: 0.8935 (mp10) cc_final: 0.8616 (mp10) REVERT: O 87 ASP cc_start: 0.8927 (m-30) cc_final: 0.8608 (m-30) REVERT: O 94 ASP cc_start: 0.8101 (t70) cc_final: 0.7504 (t70) REVERT: O 108 LYS cc_start: 0.8803 (tptm) cc_final: 0.8420 (tptp) outliers start: 64 outliers final: 32 residues processed: 326 average time/residue: 1.3809 time to fit residues: 495.5754 Evaluate side-chains 321 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 71 THR 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 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG 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 106 ASP 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 95 MET Chi-restraints excluded: chain D residue 110 ASP 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 L residue 551 GLN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056557 restraints weight = 46199.311| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.33 r_work: 0.2895 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17433 Z= 0.268 Angle : 0.664 9.334 23718 Z= 0.336 Chirality : 0.044 0.174 2634 Planarity : 0.004 0.039 3000 Dihedral : 7.531 60.230 2781 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.59 % Allowed : 18.54 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2127 helix: 1.12 (0.41), residues: 156 sheet: -0.28 (0.18), residues: 831 loop : -0.19 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 99 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE N 70 TYR 0.028 0.002 TYR E 51 ARG 0.010 0.001 ARG N 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 6) link_NAG-ASN : angle 2.49819 ( 18) link_ALPHA1-6 : bond 0.00463 ( 3) link_ALPHA1-6 : angle 2.50706 ( 9) link_BETA1-4 : bond 0.00115 ( 6) link_BETA1-4 : angle 2.34642 ( 18) link_ALPHA1-3 : bond 0.00402 ( 6) link_ALPHA1-3 : angle 2.03293 ( 18) hydrogen bonds : bond 0.03697 ( 516) hydrogen bonds : angle 5.39595 ( 1410) SS BOND : bond 0.00391 ( 21) SS BOND : angle 0.44460 ( 42) covalent geometry : bond 0.00598 (17391) covalent geometry : angle 0.65411 (23613) *********************** 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: 64 poor density : 301 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8628 (mt0) cc_final: 0.8080 (mm-40) REVERT: F 56 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8183 (mmtm) REVERT: F 127 ASP cc_start: 0.8468 (p0) cc_final: 0.8046 (p0) REVERT: G 523 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7161 (tm-30) REVERT: H 40 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7960 (tpp80) REVERT: H 89 GLU cc_start: 0.8183 (pp20) cc_final: 0.7979 (pp20) REVERT: H 146 HIS cc_start: 0.7458 (m90) cc_final: 0.7197 (m90) REVERT: I 6 GLU cc_start: 0.8097 (mp0) cc_final: 0.7583 (mp0) REVERT: I 46 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: I 85 MET cc_start: 0.8495 (mtt) cc_final: 0.8262 (mtt) REVERT: I 87 ASN cc_start: 0.8944 (t0) cc_final: 0.8684 (t0) REVERT: I 95 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7717 (ttm) REVERT: I 114 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7491 (mtm110) REVERT: I 117 LEU cc_start: 0.9084 (tt) cc_final: 0.8839 (tm) REVERT: J 16 GLN cc_start: 0.8146 (pt0) cc_final: 0.7831 (pt0) REVERT: J 26 TYR cc_start: 0.9420 (p90) cc_final: 0.9093 (p90) REVERT: J 41 LEU cc_start: 0.8679 (mt) cc_final: 0.8393 (mm) REVERT: J 51 TYR cc_start: 0.9030 (p90) cc_final: 0.8793 (p90) REVERT: J 68 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8512 (tmmm) REVERT: J 87 ASP cc_start: 0.8880 (m-30) cc_final: 0.8558 (m-30) REVERT: J 96 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8375 (mtm-85) REVERT: J 98 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8241 (mpp80) REVERT: A 56 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8251 (mmtm) REVERT: A 112 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8550 (mt-10) REVERT: B 523 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 551 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: C 13 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8731 (mmmm) REVERT: C 41 PRO cc_start: 0.8728 (Cg_exo) cc_final: 0.8480 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8662 (mt-10) REVERT: C 54 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7192 (ttm110) REVERT: C 213 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8650 (mm) REVERT: D 25 SER cc_start: 0.8848 (m) cc_final: 0.8323 (p) REVERT: D 46 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: D 87 ASN cc_start: 0.9009 (t0) cc_final: 0.8750 (t0) REVERT: E 81 GLN cc_start: 0.8765 (mp10) cc_final: 0.8372 (mp10) REVERT: E 85 GLU cc_start: 0.8336 (tt0) cc_final: 0.8053 (tt0) REVERT: E 87 ASP cc_start: 0.8775 (m-30) cc_final: 0.8355 (m-30) REVERT: E 98 ARG cc_start: 0.8495 (mpp80) cc_final: 0.8282 (mpp80) REVERT: E 108 LYS cc_start: 0.8838 (tptm) cc_final: 0.8503 (tptp) REVERT: K 44 GLN cc_start: 0.8378 (mt0) cc_final: 0.7796 (mm-40) REVERT: L 523 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7353 (tm-30) REVERT: L 545 GLU cc_start: 0.8572 (mp0) cc_final: 0.8210 (mp0) REVERT: M 11 LEU cc_start: 0.8899 (tp) cc_final: 0.8689 (tp) REVERT: M 41 PRO cc_start: 0.8718 (Cg_exo) cc_final: 0.8495 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8311 (t0) cc_final: 0.7977 (t0) REVERT: M 156 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8117 (ttp80) REVERT: N 6 GLU cc_start: 0.8034 (mp0) cc_final: 0.7617 (mp0) REVERT: N 46 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7533 (tm-30) REVERT: N 85 MET cc_start: 0.8443 (mtt) cc_final: 0.7936 (mtt) REVERT: N 87 ASN cc_start: 0.8980 (t0) cc_final: 0.8731 (t0) REVERT: N 95 MET cc_start: 0.8628 (mtp) cc_final: 0.7659 (ttm) REVERT: N 114 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7676 (mtm110) REVERT: O 16 GLN cc_start: 0.8278 (pt0) cc_final: 0.8022 (pp30) REVERT: O 81 GLN cc_start: 0.8893 (mp10) cc_final: 0.8586 (mp10) REVERT: O 94 ASP cc_start: 0.8176 (t70) cc_final: 0.7602 (t70) REVERT: O 96 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8542 (mtm-85) REVERT: O 108 LYS cc_start: 0.8807 (tptm) cc_final: 0.8494 (tptp) outliers start: 64 outliers final: 30 residues processed: 331 average time/residue: 1.3935 time to fit residues: 510.1803 Evaluate side-chains 321 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 72 MET 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 0 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 100 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058592 restraints weight = 45945.757| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.25 r_work: 0.2961 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17433 Z= 0.147 Angle : 0.631 9.465 23718 Z= 0.315 Chirality : 0.043 0.168 2634 Planarity : 0.004 0.037 3000 Dihedral : 7.069 59.897 2781 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.08 % Allowed : 19.61 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2127 helix: 1.26 (0.42), residues: 156 sheet: -0.01 (0.19), residues: 735 loop : -0.23 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.002 0.000 HIS H 35 PHE 0.007 0.001 PHE M 211 TYR 0.029 0.001 TYR E 51 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 6) link_NAG-ASN : angle 2.18762 ( 18) link_ALPHA1-6 : bond 0.00044 ( 3) link_ALPHA1-6 : angle 2.06951 ( 9) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 2.26084 ( 18) link_ALPHA1-3 : bond 0.00751 ( 6) link_ALPHA1-3 : angle 1.72647 ( 18) hydrogen bonds : bond 0.03188 ( 516) hydrogen bonds : angle 5.19349 ( 1410) SS BOND : bond 0.00242 ( 21) SS BOND : angle 0.35901 ( 42) covalent geometry : bond 0.00330 (17391) covalent geometry : angle 0.62312 (23613) *********************** 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 357 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 302 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8628 (mt0) cc_final: 0.8100 (mm-40) REVERT: F 54 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8016 (ptm-80) REVERT: F 56 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8191 (mmtm) REVERT: F 100 GLU cc_start: 0.8756 (mp0) cc_final: 0.8516 (mp0) REVERT: F 127 ASP cc_start: 0.8377 (p0) cc_final: 0.7924 (p0) REVERT: G 523 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7236 (tm-30) REVERT: H 89 GLU cc_start: 0.8225 (pp20) cc_final: 0.8005 (pp20) REVERT: H 90 ASP cc_start: 0.6858 (m-30) cc_final: 0.6628 (m-30) REVERT: H 156 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8347 (ttp80) REVERT: I 6 GLU cc_start: 0.8032 (mp0) cc_final: 0.7710 (mp0) REVERT: I 46 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: I 87 ASN cc_start: 0.8967 (t0) cc_final: 0.8725 (t0) REVERT: I 95 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7867 (ttm) REVERT: I 104 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8347 (mpp-170) REVERT: I 114 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7634 (mtm110) REVERT: I 117 LEU cc_start: 0.9117 (tt) cc_final: 0.8883 (tm) REVERT: J 16 GLN cc_start: 0.7778 (pt0) cc_final: 0.7422 (pt0) REVERT: J 26 TYR cc_start: 0.9425 (p90) cc_final: 0.9154 (p90) REVERT: J 87 ASP cc_start: 0.8885 (m-30) cc_final: 0.8547 (m-30) REVERT: J 94 ASP cc_start: 0.8108 (t0) cc_final: 0.7826 (t70) REVERT: J 96 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8390 (mtm-85) REVERT: J 98 ARG cc_start: 0.8530 (mtt90) cc_final: 0.8103 (mpp80) REVERT: B 523 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 551 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7438 (pp30) REVERT: C 13 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8717 (mmmm) REVERT: C 34 MET cc_start: 0.9408 (mmm) cc_final: 0.9188 (tpt) REVERT: C 40 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7766 (tpp80) REVERT: C 41 PRO cc_start: 0.8729 (Cg_exo) cc_final: 0.7521 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8044 (mm110) REVERT: C 46 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8700 (mt-10) REVERT: C 54 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7156 (ttm170) REVERT: C 89 GLU cc_start: 0.8165 (pp20) cc_final: 0.7877 (pp20) REVERT: C 213 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8618 (mm) REVERT: D 25 SER cc_start: 0.8855 (m) cc_final: 0.8316 (p) REVERT: D 46 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 87 ASN cc_start: 0.9035 (t0) cc_final: 0.8833 (t0) REVERT: D 95 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: E 81 GLN cc_start: 0.8830 (mp10) cc_final: 0.8454 (mp10) REVERT: E 85 GLU cc_start: 0.8369 (tt0) cc_final: 0.8127 (tt0) REVERT: E 87 ASP cc_start: 0.8800 (m-30) cc_final: 0.8427 (m-30) REVERT: E 94 ASP cc_start: 0.8054 (t0) cc_final: 0.7827 (t70) REVERT: E 108 LYS cc_start: 0.8908 (tptm) cc_final: 0.8576 (tptp) REVERT: K 77 THR cc_start: 0.8862 (p) cc_final: 0.8598 (t) REVERT: L 523 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7299 (tm-30) REVERT: L 545 GLU cc_start: 0.8493 (mp0) cc_final: 0.8206 (mp0) REVERT: M 11 LEU cc_start: 0.8864 (tp) cc_final: 0.8592 (tp) REVERT: M 59 ASP cc_start: 0.8254 (t0) cc_final: 0.7964 (t0) REVERT: M 89 GLU cc_start: 0.8007 (pp20) cc_final: 0.7645 (pp20) REVERT: M 156 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8293 (ttp80) REVERT: M 213 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8555 (mm) REVERT: N 46 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7633 (tm-30) REVERT: N 87 ASN cc_start: 0.8976 (t0) cc_final: 0.8755 (t0) REVERT: N 95 MET cc_start: 0.8671 (mtp) cc_final: 0.7785 (ttm) REVERT: O 16 GLN cc_start: 0.8115 (pt0) cc_final: 0.7882 (pp30) REVERT: O 81 GLN cc_start: 0.8908 (mp10) cc_final: 0.8547 (mp10) REVERT: O 94 ASP cc_start: 0.8104 (t70) cc_final: 0.7612 (t70) REVERT: O 108 LYS cc_start: 0.8828 (tptm) cc_final: 0.8495 (tptt) outliers start: 55 outliers final: 27 residues processed: 330 average time/residue: 1.3874 time to fit residues: 506.1089 Evaluate side-chains 321 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain 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 95 MET Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL 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 95 MET Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 213 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 0.0030 chunk 206 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN A 188 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN L 586 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.076654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057955 restraints weight = 45701.984| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.23 r_work: 0.2944 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17433 Z= 0.180 Angle : 0.648 8.709 23718 Z= 0.322 Chirality : 0.043 0.172 2634 Planarity : 0.004 0.037 3000 Dihedral : 7.002 59.104 2781 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.97 % Allowed : 20.95 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2127 helix: 1.33 (0.42), residues: 156 sheet: -0.16 (0.19), residues: 756 loop : -0.26 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE N 70 TYR 0.028 0.001 TYR E 51 ARG 0.009 0.001 ARG K 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 6) link_NAG-ASN : angle 2.20612 ( 18) link_ALPHA1-6 : bond 0.00132 ( 3) link_ALPHA1-6 : angle 2.13567 ( 9) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 2.34209 ( 18) link_ALPHA1-3 : bond 0.00599 ( 6) link_ALPHA1-3 : angle 1.88587 ( 18) hydrogen bonds : bond 0.03256 ( 516) hydrogen bonds : angle 5.13774 ( 1410) SS BOND : bond 0.00244 ( 21) SS BOND : angle 0.33114 ( 42) covalent geometry : bond 0.00406 (17391) covalent geometry : angle 0.63927 (23613) *********************** 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 348 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8619 (mt0) cc_final: 0.8077 (mm-40) REVERT: F 54 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8068 (ptm-80) REVERT: F 56 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8203 (mmtm) REVERT: F 100 GLU cc_start: 0.8771 (mp0) cc_final: 0.8512 (mp0) REVERT: F 127 ASP cc_start: 0.8412 (p0) cc_final: 0.7984 (p0) REVERT: G 523 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7189 (tm-30) REVERT: H 90 ASP cc_start: 0.6805 (m-30) cc_final: 0.6533 (m-30) REVERT: H 146 HIS cc_start: 0.7487 (m90) cc_final: 0.7219 (m90) REVERT: I 46 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: I 87 ASN cc_start: 0.8976 (t0) cc_final: 0.8757 (t0) REVERT: I 95 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7816 (ttm) REVERT: I 104 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8317 (mpp80) REVERT: I 117 LEU cc_start: 0.9095 (tt) cc_final: 0.8848 (tm) REVERT: J 16 GLN cc_start: 0.7846 (pt0) cc_final: 0.7507 (pt0) REVERT: J 26 TYR cc_start: 0.9422 (p90) cc_final: 0.9130 (p90) REVERT: J 87 ASP cc_start: 0.8876 (m-30) cc_final: 0.8564 (m-30) REVERT: J 94 ASP cc_start: 0.8103 (t0) cc_final: 0.7837 (t70) REVERT: J 96 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8411 (mtm-85) REVERT: J 98 ARG cc_start: 0.8579 (mtt90) cc_final: 0.8158 (mpp80) REVERT: A 56 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8244 (mmtm) REVERT: B 523 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 551 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: C 13 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8725 (mmmm) REVERT: C 34 MET cc_start: 0.9418 (mmm) cc_final: 0.9190 (tpt) REVERT: C 41 PRO cc_start: 0.8744 (Cg_exo) cc_final: 0.7741 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8023 (mm110) REVERT: C 46 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8700 (mt-10) REVERT: C 59 ASP cc_start: 0.8341 (t0) cc_final: 0.8113 (t0) REVERT: C 62 GLU cc_start: 0.8493 (pt0) cc_final: 0.8089 (pm20) REVERT: C 89 GLU cc_start: 0.8189 (pp20) cc_final: 0.7885 (pp20) REVERT: C 139 ASP cc_start: 0.8519 (p0) cc_final: 0.8315 (p0) REVERT: C 213 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8652 (mm) REVERT: D 25 SER cc_start: 0.8788 (m) cc_final: 0.8286 (p) REVERT: D 46 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 95 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: E 68 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8180 (tmmm) REVERT: E 85 GLU cc_start: 0.8369 (tt0) cc_final: 0.8127 (tt0) REVERT: E 87 ASP cc_start: 0.8832 (m-30) cc_final: 0.8473 (m-30) REVERT: E 94 ASP cc_start: 0.8161 (t0) cc_final: 0.7921 (t70) REVERT: E 108 LYS cc_start: 0.8904 (tptm) cc_final: 0.8561 (tptp) REVERT: E 109 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8326 (tp) REVERT: L 522 ASP cc_start: 0.7523 (t70) cc_final: 0.7151 (t0) REVERT: L 545 GLU cc_start: 0.8545 (mp0) cc_final: 0.8232 (mp0) REVERT: M 11 LEU cc_start: 0.8837 (tp) cc_final: 0.8597 (tp) REVERT: M 59 ASP cc_start: 0.8250 (t0) cc_final: 0.7923 (t0) REVERT: M 156 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8294 (ttp80) REVERT: M 213 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8610 (mm) REVERT: N 46 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7592 (tm-30) REVERT: N 87 ASN cc_start: 0.8947 (t0) cc_final: 0.8742 (t0) REVERT: N 95 MET cc_start: 0.8683 (mtp) cc_final: 0.7688 (ttm) REVERT: O 16 GLN cc_start: 0.8111 (pt0) cc_final: 0.7867 (pp30) REVERT: O 81 GLN cc_start: 0.8901 (mp10) cc_final: 0.8565 (mp10) REVERT: O 94 ASP cc_start: 0.8159 (t70) cc_final: 0.7697 (t70) REVERT: O 108 LYS cc_start: 0.8855 (tptm) cc_final: 0.8511 (tptt) outliers start: 53 outliers final: 29 residues processed: 321 average time/residue: 1.3901 time to fit residues: 492.3443 Evaluate side-chains 321 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain 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 95 MET Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL 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 95 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain K residue 78 ASP 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 91 SER Chi-restraints excluded: chain M residue 213 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 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 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 = 0.3535 r_free = 0.3535 target = 0.078174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058810 restraints weight = 45333.796| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.31 r_work: 0.2949 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3524 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= 0.147 Angle : 0.659 8.682 23718 Z= 0.330 Chirality : 0.043 0.167 2634 Planarity : 0.005 0.090 3000 Dihedral : 6.807 58.178 2781 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.80 % Allowed : 22.24 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2127 helix: 1.43 (0.43), residues: 156 sheet: -0.06 (0.19), residues: 738 loop : -0.22 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.000 HIS H 35 PHE 0.009 0.001 PHE I 70 TYR 0.032 0.001 TYR J 51 ARG 0.022 0.001 ARG I 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 6) link_NAG-ASN : angle 2.06312 ( 18) link_ALPHA1-6 : bond 0.00065 ( 3) link_ALPHA1-6 : angle 2.00477 ( 9) link_BETA1-4 : bond 0.00397 ( 6) link_BETA1-4 : angle 2.40222 ( 18) link_ALPHA1-3 : bond 0.00742 ( 6) link_ALPHA1-3 : angle 1.80150 ( 18) hydrogen bonds : bond 0.03091 ( 516) hydrogen bonds : angle 5.06366 ( 1410) SS BOND : bond 0.00184 ( 21) SS BOND : angle 0.33630 ( 42) covalent geometry : bond 0.00334 (17391) covalent geometry : angle 0.65179 (23613) *********************** 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 346 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8581 (mt0) cc_final: 0.8045 (mm-40) REVERT: F 54 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8044 (ptm-80) REVERT: F 56 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8165 (mmtm) REVERT: F 100 GLU cc_start: 0.8730 (mp0) cc_final: 0.8528 (mp0) REVERT: F 127 ASP cc_start: 0.8451 (p0) cc_final: 0.8067 (p0) REVERT: G 523 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7211 (tm-30) REVERT: G 551 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7664 (pp30) REVERT: H 80 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: H 146 HIS cc_start: 0.7447 (m90) cc_final: 0.7164 (m90) REVERT: I 46 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: I 85 MET cc_start: 0.8488 (mpp) cc_final: 0.8176 (mpp) REVERT: I 95 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7790 (ttm) REVERT: I 117 LEU cc_start: 0.9089 (tt) cc_final: 0.8817 (tm) REVERT: J 16 GLN cc_start: 0.7951 (pt0) cc_final: 0.7619 (pt0) REVERT: J 26 TYR cc_start: 0.9421 (p90) cc_final: 0.9130 (p90) REVERT: J 41 LEU cc_start: 0.8696 (mt) cc_final: 0.8439 (mm) REVERT: J 87 ASP cc_start: 0.8896 (m-30) cc_final: 0.8553 (m-30) REVERT: J 94 ASP cc_start: 0.8115 (t0) cc_final: 0.7852 (t70) REVERT: J 96 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8431 (mtm-85) REVERT: J 98 ARG cc_start: 0.8543 (mtt90) cc_final: 0.8099 (mpp80) REVERT: A 56 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8195 (mmtm) REVERT: B 523 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 551 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7302 (pp30) REVERT: C 13 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8743 (mmmm) REVERT: C 34 MET cc_start: 0.9435 (mmm) cc_final: 0.9200 (tpt) REVERT: C 41 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.7376 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8028 (mm110) REVERT: C 46 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8666 (mt-10) REVERT: C 54 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7152 (ttm110) REVERT: C 59 ASP cc_start: 0.8390 (t0) cc_final: 0.8123 (t0) REVERT: C 62 GLU cc_start: 0.8534 (pt0) cc_final: 0.8094 (pm20) REVERT: C 139 ASP cc_start: 0.8524 (p0) cc_final: 0.8307 (p0) REVERT: C 213 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8549 (mm) REVERT: D 25 SER cc_start: 0.8759 (m) cc_final: 0.8217 (p) REVERT: D 39 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 46 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: D 95 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7502 (ttm) REVERT: E 68 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8144 (tmmm) REVERT: E 85 GLU cc_start: 0.8333 (tt0) cc_final: 0.8081 (tt0) REVERT: E 94 ASP cc_start: 0.8055 (t0) cc_final: 0.7839 (t70) REVERT: E 108 LYS cc_start: 0.8876 (tptm) cc_final: 0.8530 (tptp) REVERT: E 109 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8399 (tp) REVERT: K 77 THR cc_start: 0.8841 (p) cc_final: 0.8592 (t) REVERT: L 545 GLU cc_start: 0.8513 (mp0) cc_final: 0.8170 (mp0) REVERT: M 11 LEU cc_start: 0.8914 (tp) cc_final: 0.8669 (tp) REVERT: M 59 ASP cc_start: 0.8232 (t0) cc_final: 0.7958 (t0) REVERT: M 156 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8261 (ttp80) REVERT: M 213 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8524 (mm) REVERT: N 39 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8446 (tm-30) REVERT: N 46 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7591 (tm-30) REVERT: N 95 MET cc_start: 0.8621 (mtp) cc_final: 0.7631 (ttm) REVERT: O 16 GLN cc_start: 0.8173 (pt0) cc_final: 0.7909 (pp30) REVERT: O 81 GLN cc_start: 0.8906 (mp10) cc_final: 0.8524 (mp10) REVERT: O 94 ASP cc_start: 0.8157 (t70) cc_final: 0.7675 (t70) REVERT: O 108 LYS cc_start: 0.8786 (tptm) cc_final: 0.8463 (tptt) outliers start: 50 outliers final: 29 residues processed: 324 average time/residue: 1.4403 time to fit residues: 514.4740 Evaluate side-chains 323 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain 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 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL 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 95 MET 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 78 ASP 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 198 ASP Chi-restraints excluded: chain M residue 213 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 chunk 185 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 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 = 0.3510 r_free = 0.3510 target = 0.076969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057498 restraints weight = 46136.100| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.32 r_work: 0.2916 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17433 Z= 0.227 Angle : 0.698 9.051 23718 Z= 0.351 Chirality : 0.044 0.180 2634 Planarity : 0.005 0.058 3000 Dihedral : 6.871 57.761 2781 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.80 % Allowed : 22.46 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2127 helix: 1.42 (0.42), residues: 156 sheet: -0.21 (0.19), residues: 768 loop : -0.24 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE N 70 TYR 0.029 0.001 TYR E 51 ARG 0.014 0.001 ARG I 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 2.21791 ( 18) link_ALPHA1-6 : bond 0.00307 ( 3) link_ALPHA1-6 : angle 2.22221 ( 9) link_BETA1-4 : bond 0.00217 ( 6) link_BETA1-4 : angle 2.56074 ( 18) link_ALPHA1-3 : bond 0.00549 ( 6) link_ALPHA1-3 : angle 1.92770 ( 18) hydrogen bonds : bond 0.03285 ( 516) hydrogen bonds : angle 5.06859 ( 1410) SS BOND : bond 0.00286 ( 21) SS BOND : angle 0.34045 ( 42) covalent geometry : bond 0.00513 (17391) covalent geometry : angle 0.68960 (23613) *********************** 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 341 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8565 (mt0) cc_final: 0.8018 (mm-40) REVERT: F 54 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8065 (ptm-80) REVERT: F 56 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8181 (mmtm) REVERT: F 100 GLU cc_start: 0.8764 (mp0) cc_final: 0.8539 (mp0) REVERT: F 127 ASP cc_start: 0.8476 (p0) cc_final: 0.8060 (p0) REVERT: G 523 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7256 (tm-30) REVERT: G 551 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7652 (pp30) REVERT: H 146 HIS cc_start: 0.7496 (m90) cc_final: 0.7202 (m90) REVERT: I 46 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: I 95 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: I 117 LEU cc_start: 0.9045 (tt) cc_final: 0.8779 (tm) REVERT: J 16 GLN cc_start: 0.8020 (pt0) cc_final: 0.7700 (pt0) REVERT: J 26 TYR cc_start: 0.9422 (p90) cc_final: 0.9067 (p90) REVERT: J 41 LEU cc_start: 0.8650 (mt) cc_final: 0.8390 (mm) REVERT: J 87 ASP cc_start: 0.8861 (m-30) cc_final: 0.8530 (m-30) REVERT: J 94 ASP cc_start: 0.8086 (t0) cc_final: 0.7831 (t70) REVERT: J 96 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8388 (mtm-85) REVERT: J 98 ARG cc_start: 0.8606 (mtt90) cc_final: 0.8171 (mpp80) REVERT: A 56 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8187 (mmtm) REVERT: A 156 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8598 (mm-30) REVERT: B 523 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 551 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7392 (pp30) REVERT: C 13 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8741 (mmmm) REVERT: C 34 MET cc_start: 0.9442 (mmm) cc_final: 0.9200 (tpt) REVERT: C 41 PRO cc_start: 0.8677 (Cg_exo) cc_final: 0.7357 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8078 (mm110) REVERT: C 46 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 54 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7136 (ttm110) REVERT: C 59 ASP cc_start: 0.8447 (t0) cc_final: 0.8172 (t0) REVERT: C 62 GLU cc_start: 0.8561 (pt0) cc_final: 0.7981 (pp20) REVERT: C 139 ASP cc_start: 0.8563 (p0) cc_final: 0.8342 (p0) REVERT: C 213 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 25 SER cc_start: 0.8778 (m) cc_final: 0.8274 (p) REVERT: D 39 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 46 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: D 67 ARG cc_start: 0.7840 (pmt-80) cc_final: 0.7020 (tpp80) REVERT: D 95 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7496 (ttm) REVERT: E 52 ASP cc_start: 0.8495 (t0) cc_final: 0.8254 (t0) REVERT: E 85 GLU cc_start: 0.8389 (tt0) cc_final: 0.8095 (tt0) REVERT: E 94 ASP cc_start: 0.8100 (t0) cc_final: 0.7864 (t70) REVERT: E 108 LYS cc_start: 0.8844 (tptm) cc_final: 0.8529 (tptp) REVERT: E 109 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8420 (tp) REVERT: K 50 LYS cc_start: 0.7025 (mmmt) cc_final: 0.6753 (mmmt) REVERT: K 77 THR cc_start: 0.8830 (p) cc_final: 0.8587 (t) REVERT: L 545 GLU cc_start: 0.8532 (mp0) cc_final: 0.8182 (mp0) REVERT: M 11 LEU cc_start: 0.8895 (tp) cc_final: 0.8682 (tp) REVERT: M 59 ASP cc_start: 0.8202 (t0) cc_final: 0.7906 (t0) REVERT: M 156 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8250 (ttp80) REVERT: M 213 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8552 (mm) REVERT: N 39 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8449 (tm-30) REVERT: N 46 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7548 (tm-30) REVERT: N 85 MET cc_start: 0.8587 (mmm) cc_final: 0.8040 (mmm) REVERT: N 95 MET cc_start: 0.8655 (mtp) cc_final: 0.7618 (ttm) REVERT: O 16 GLN cc_start: 0.8236 (pt0) cc_final: 0.7990 (pp30) REVERT: O 39 GLN cc_start: 0.9080 (tt0) cc_final: 0.8876 (tm-30) REVERT: O 81 GLN cc_start: 0.8882 (mp10) cc_final: 0.8466 (mp10) REVERT: O 94 ASP cc_start: 0.8220 (t70) cc_final: 0.7704 (t70) REVERT: O 108 LYS cc_start: 0.8807 (tptm) cc_final: 0.8482 (tptt) outliers start: 50 outliers final: 28 residues processed: 322 average time/residue: 1.3846 time to fit residues: 492.8857 Evaluate side-chains 324 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL 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 95 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 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 213 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 0.0370 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 0.0050 chunk 161 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3528 r_free = 0.3528 target = 0.077875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059317 restraints weight = 45951.132| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.25 r_work: 0.2968 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3611 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= 0.139 Angle : 0.692 9.932 23718 Z= 0.346 Chirality : 0.043 0.161 2634 Planarity : 0.004 0.056 3000 Dihedral : 6.580 56.639 2781 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.35 % Allowed : 23.14 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2127 helix: 1.44 (0.43), residues: 156 sheet: -0.15 (0.19), residues: 753 loop : -0.26 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE N 70 TYR 0.031 0.001 TYR J 51 ARG 0.016 0.001 ARG I 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 6) link_NAG-ASN : angle 1.96146 ( 18) link_ALPHA1-6 : bond 0.00163 ( 3) link_ALPHA1-6 : angle 1.97912 ( 9) link_BETA1-4 : bond 0.00527 ( 6) link_BETA1-4 : angle 2.48417 ( 18) link_ALPHA1-3 : bond 0.00834 ( 6) link_ALPHA1-3 : angle 1.70716 ( 18) hydrogen bonds : bond 0.02968 ( 516) hydrogen bonds : angle 4.97308 ( 1410) SS BOND : bond 0.00212 ( 21) SS BOND : angle 0.75143 ( 42) covalent geometry : bond 0.00320 (17391) covalent geometry : angle 0.68501 (23613) ********************** 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 339 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8605 (mt0) cc_final: 0.8053 (mm-40) REVERT: F 54 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8052 (ptm-80) REVERT: F 56 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8165 (mmtm) REVERT: F 100 GLU cc_start: 0.8783 (mp0) cc_final: 0.8566 (mp0) REVERT: F 127 ASP cc_start: 0.8399 (p0) cc_final: 0.8090 (p0) REVERT: G 523 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7262 (tm-30) REVERT: G 545 GLU cc_start: 0.7762 (pp20) cc_final: 0.7443 (tm-30) REVERT: G 551 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7511 (pp30) REVERT: H 80 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: H 146 HIS cc_start: 0.7429 (m90) cc_final: 0.7152 (m90) REVERT: H 156 ARG cc_start: 0.8840 (tmt90) cc_final: 0.8504 (ttp80) REVERT: I 39 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8258 (tm-30) REVERT: I 46 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: I 85 MET cc_start: 0.8404 (mpp) cc_final: 0.7923 (mpp) REVERT: I 95 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7810 (ttm) REVERT: I 117 LEU cc_start: 0.9091 (tt) cc_final: 0.8838 (tm) REVERT: J 16 GLN cc_start: 0.7846 (pt0) cc_final: 0.7517 (pt0) REVERT: J 26 TYR cc_start: 0.9435 (p90) cc_final: 0.9138 (p90) REVERT: J 47 LYS cc_start: 0.9083 (tttp) cc_final: 0.8848 (tttt) REVERT: J 87 ASP cc_start: 0.8873 (m-30) cc_final: 0.8534 (m-30) REVERT: J 94 ASP cc_start: 0.8031 (t0) cc_final: 0.7741 (t70) REVERT: J 96 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8391 (mtm-85) REVERT: J 98 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8070 (mpp80) REVERT: A 56 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8207 (mmtm) REVERT: A 100 GLU cc_start: 0.8636 (mp0) cc_final: 0.8435 (mp0) REVERT: A 156 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8486 (mm-30) REVERT: B 523 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 551 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7320 (pp30) REVERT: C 13 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8734 (mmmm) REVERT: C 34 MET cc_start: 0.9449 (mmm) cc_final: 0.9219 (tpt) REVERT: C 40 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7797 (tpp80) REVERT: C 41 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.7626 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7962 (mm110) REVERT: C 46 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8645 (mt-10) REVERT: C 59 ASP cc_start: 0.8417 (t0) cc_final: 0.8114 (t0) REVERT: C 62 GLU cc_start: 0.8490 (pt0) cc_final: 0.8090 (pm20) REVERT: C 139 ASP cc_start: 0.8559 (p0) cc_final: 0.7997 (p0) REVERT: C 213 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8557 (mm) REVERT: D 25 SER cc_start: 0.8807 (m) cc_final: 0.8331 (p) REVERT: D 39 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 46 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: D 95 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7491 (ttm) REVERT: E 52 ASP cc_start: 0.8401 (t0) cc_final: 0.8154 (t0) REVERT: E 68 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8132 (tmmm) REVERT: E 85 GLU cc_start: 0.8390 (tt0) cc_final: 0.8137 (tt0) REVERT: E 94 ASP cc_start: 0.8004 (t0) cc_final: 0.7801 (t70) REVERT: E 108 LYS cc_start: 0.8891 (tptm) cc_final: 0.8593 (tptp) REVERT: E 109 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8454 (tp) REVERT: K 50 LYS cc_start: 0.7189 (mmmt) cc_final: 0.6880 (mmmt) REVERT: L 545 GLU cc_start: 0.8466 (mp0) cc_final: 0.8150 (mp0) REVERT: M 13 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8757 (mmmt) REVERT: M 43 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8235 (mm110) REVERT: M 54 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7176 (ttm170) REVERT: M 59 ASP cc_start: 0.8213 (t0) cc_final: 0.7953 (t0) REVERT: M 80 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: M 156 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8274 (ttp80) REVERT: M 213 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8511 (mm) REVERT: N 39 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8443 (tm-30) REVERT: N 46 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7496 (tm-30) REVERT: N 85 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: N 95 MET cc_start: 0.8660 (mtp) cc_final: 0.7648 (ttm) REVERT: O 16 GLN cc_start: 0.8054 (pt0) cc_final: 0.7812 (pp30) REVERT: O 81 GLN cc_start: 0.8906 (mp10) cc_final: 0.8477 (mp10) REVERT: O 94 ASP cc_start: 0.8086 (t70) cc_final: 0.7372 (t70) REVERT: O 108 LYS cc_start: 0.8807 (tptm) cc_final: 0.8482 (tptt) outliers start: 42 outliers final: 24 residues processed: 322 average time/residue: 1.3944 time to fit residues: 495.1424 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 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 142 VAL 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 95 MET Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL 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 95 MET 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 78 ASP 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 213 ILE Chi-restraints excluded: chain M residue 232 THR 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 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 0.0040 chunk 141 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 HIS O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059120 restraints weight = 45787.491| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.24 r_work: 0.2976 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17433 Z= 0.150 Angle : 0.694 10.053 23718 Z= 0.346 Chirality : 0.043 0.164 2634 Planarity : 0.004 0.049 3000 Dihedral : 6.539 56.013 2781 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.52 % Allowed : 23.42 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2127 helix: 1.43 (0.42), residues: 156 sheet: -0.13 (0.19), residues: 753 loop : -0.26 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS M 146 PHE 0.011 0.001 PHE N 70 TYR 0.033 0.001 TYR J 51 ARG 0.015 0.001 ARG I 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 6) link_NAG-ASN : angle 1.94939 ( 18) link_ALPHA1-6 : bond 0.00018 ( 3) link_ALPHA1-6 : angle 1.90989 ( 9) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 2.49698 ( 18) link_ALPHA1-3 : bond 0.00740 ( 6) link_ALPHA1-3 : angle 1.79605 ( 18) hydrogen bonds : bond 0.03023 ( 516) hydrogen bonds : angle 4.93169 ( 1410) SS BOND : bond 0.00186 ( 21) SS BOND : angle 0.93806 ( 42) covalent geometry : bond 0.00346 (17391) covalent geometry : angle 0.68630 (23613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12108.59 seconds wall clock time: 209 minutes 21.50 seconds (12561.50 seconds total)