Starting phenix.real_space_refine on Wed Jun 18 18:16:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpm_27638/06_2025/8dpm_27638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpm_27638/06_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_27638/06_2025/8dpm_27638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpm_27638/06_2025/8dpm_27638.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpm_27638/06_2025/8dpm_27638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpm_27638/06_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): 1.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.59, per 1000 atoms: 0.62 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: 4.30 Conformation dependent library (CDL) restraints added in 2.4 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: 2.85 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: 5.95 Time building geometry restraints manager: 5.07 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: 4.380 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.120 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 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:14.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.510 ------------------------------------------------------------------------------- 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 : 1.943 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: 1.3232 time to fit residues: 698.8931 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 : 1.946 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056224 restraints weight = 46403.912| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.32 r_work: 0.2872 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8568 (mt0) cc_final: 0.7939 (mm-40) REVERT: F 54 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8074 (ptm160) REVERT: F 100 GLU cc_start: 0.8667 (mp0) cc_final: 0.8412 (mp0) REVERT: F 136 ARG cc_start: 0.8457 (tpt90) cc_final: 0.8003 (tmt-80) REVERT: G 523 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7140 (tm-30) REVERT: I 6 GLU cc_start: 0.7861 (mp0) cc_final: 0.7383 (mp0) REVERT: I 46 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 67 ARG cc_start: 0.6844 (tpp-160) cc_final: 0.6644 (tpp-160) REVERT: I 117 LEU cc_start: 0.9068 (tt) cc_final: 0.8837 (tm) REVERT: J 16 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: J 26 TYR cc_start: 0.9452 (p90) cc_final: 0.9133 (p90) REVERT: J 44 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8717 (p) REVERT: J 83 GLU cc_start: 0.8759 (pt0) cc_final: 0.8501 (pm20) REVERT: J 96 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8345 (mtm-85) REVERT: A 56 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8205 (mmtm) REVERT: A 114 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: B 523 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 551 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7421 (pp30) REVERT: C 80 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6881 (p90) REVERT: C 213 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (mm) REVERT: D 25 SER cc_start: 0.8962 (m) cc_final: 0.8320 (p) REVERT: D 43 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8274 (mmmm) REVERT: D 46 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 75 ASP cc_start: 0.8732 (t0) cc_final: 0.8410 (p0) REVERT: D 80 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8718 (mtpm) REVERT: D 87 ASN cc_start: 0.8905 (t0) cc_final: 0.8693 (t0) REVERT: D 110 ASP cc_start: 0.7894 (m-30) cc_final: 0.7674 (m-30) REVERT: E 83 GLU cc_start: 0.8627 (pt0) cc_final: 0.8427 (pm20) REVERT: E 85 GLU cc_start: 0.8301 (tt0) cc_final: 0.8069 (tt0) REVERT: E 87 ASP cc_start: 0.8772 (m-30) cc_final: 0.8442 (m-30) REVERT: K 54 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: L 523 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7297 (tm-30) REVERT: L 545 GLU cc_start: 0.8548 (mp0) cc_final: 0.8309 (mp0) REVERT: M 59 ASP cc_start: 0.8451 (t0) cc_final: 0.7997 (t0) REVERT: M 156 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8310 (ttp80) REVERT: N 28 THR cc_start: 0.8799 (m) cc_final: 0.8498 (t) REVERT: N 43 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8480 (mmmm) REVERT: N 46 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7530 (tm-30) REVERT: N 61 ASP cc_start: 0.8031 (t0) cc_final: 0.7736 (t0) REVERT: N 67 ARG cc_start: 0.6995 (tpp-160) cc_final: 0.6554 (tpp-160) REVERT: N 95 MET cc_start: 0.8528 (mtp) cc_final: 0.7638 (ttm) REVERT: O 16 GLN cc_start: 0.8390 (pt0) cc_final: 0.8129 (pp30) REVERT: O 44 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8652 (p) REVERT: O 85 GLU cc_start: 0.8425 (tt0) cc_final: 0.8083 (tt0) REVERT: O 108 LYS cc_start: 0.8768 (tptm) cc_final: 0.8369 (tptp) outliers start: 78 outliers final: 31 residues processed: 348 average time/residue: 1.4352 time to fit residues: 550.5247 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 : 1.837 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 O 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.077838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059222 restraints weight = 45653.145| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.22 r_work: 0.2968 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17433 Z= 0.150 Angle : 0.618 7.895 23718 Z= 0.310 Chirality : 0.043 0.157 2634 Planarity : 0.004 0.033 3000 Dihedral : 7.720 65.072 2781 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.31 % Allowed : 18.04 % Favored : 78.66 % 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: 0.71 (0.42), residues: 156 sheet: 0.15 (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 E 51 ARG 0.008 0.001 ARG N 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 2.47902 ( 18) link_ALPHA1-6 : bond 0.00187 ( 3) link_ALPHA1-6 : angle 2.15712 ( 9) link_BETA1-4 : bond 0.00469 ( 6) link_BETA1-4 : angle 2.11927 ( 18) link_ALPHA1-3 : bond 0.00805 ( 6) link_ALPHA1-3 : angle 1.59056 ( 18) hydrogen bonds : bond 0.03754 ( 516) hydrogen bonds : angle 5.63822 ( 1410) SS BOND : bond 0.00272 ( 21) SS BOND : angle 0.45095 ( 42) covalent geometry : bond 0.00329 (17391) covalent geometry : angle 0.60917 (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 376 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: F 127 ASP cc_start: 0.8296 (p0) cc_final: 0.7873 (p0) REVERT: G 523 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7263 (tm-30) REVERT: I 6 GLU cc_start: 0.8059 (mp0) cc_final: 0.7562 (mp0) REVERT: I 43 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8306 (tttm) REVERT: I 46 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: I 87 ASN cc_start: 0.8926 (t0) cc_final: 0.8701 (t0) REVERT: I 95 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7792 (ttm) REVERT: I 114 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7404 (mtm110) REVERT: I 117 LEU cc_start: 0.9113 (tt) cc_final: 0.8909 (tm) REVERT: J 51 TYR cc_start: 0.9009 (p90) cc_final: 0.8730 (p90) REVERT: J 87 ASP cc_start: 0.8869 (m-30) cc_final: 0.8560 (m-30) REVERT: A 56 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8250 (mmtm) REVERT: A 114 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8837 (mttm) REVERT: B 523 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 551 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: C 34 MET cc_start: 0.9450 (mmm) cc_final: 0.9196 (tpt) REVERT: C 43 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7926 (mm110) REVERT: C 54 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7250 (ttm170) REVERT: C 80 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6736 (p90) REVERT: C 213 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 25 SER cc_start: 0.8756 (m) cc_final: 0.8332 (p) REVERT: D 43 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8252 (mmmm) REVERT: D 46 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: D 80 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8668 (mtpm) REVERT: D 87 ASN cc_start: 0.8937 (t0) cc_final: 0.8671 (t0) REVERT: E 85 GLU cc_start: 0.8261 (tt0) cc_final: 0.7970 (tt0) REVERT: E 87 ASP cc_start: 0.8753 (m-30) cc_final: 0.8366 (m-30) REVERT: E 94 ASP cc_start: 0.8160 (t0) cc_final: 0.7897 (t70) REVERT: E 108 LYS cc_start: 0.8819 (tptm) cc_final: 0.8494 (tptp) REVERT: K 54 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7960 (ptm160) REVERT: K 120 GLU cc_start: 0.8413 (pm20) cc_final: 0.8159 (pm20) REVERT: L 523 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7238 (tm-30) REVERT: L 545 GLU cc_start: 0.8529 (mp0) cc_final: 0.8257 (mp0) REVERT: M 59 ASP cc_start: 0.8411 (t0) cc_final: 0.8033 (t0) REVERT: M 156 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8323 (ttp80) REVERT: N 6 GLU cc_start: 0.8044 (mp0) cc_final: 0.7832 (mp0) REVERT: N 28 THR cc_start: 0.8725 (m) cc_final: 0.8395 (t) REVERT: N 43 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8403 (mmmm) REVERT: N 46 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7545 (tm-30) REVERT: N 87 ASN cc_start: 0.8791 (t0) cc_final: 0.8567 (t0) REVERT: N 95 MET cc_start: 0.8538 (mtp) cc_final: 0.7743 (ttm) REVERT: O 16 GLN cc_start: 0.8236 (pt0) cc_final: 0.8023 (pp30) REVERT: O 44 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8711 (p) REVERT: O 85 GLU cc_start: 0.8440 (tt0) cc_final: 0.8192 (tt0) REVERT: O 87 ASP cc_start: 0.8813 (m-30) cc_final: 0.8525 (m-30) REVERT: O 108 LYS cc_start: 0.8811 (tptm) cc_final: 0.8430 (tptp) outliers start: 59 outliers final: 22 residues processed: 342 average time/residue: 1.4401 time to fit residues: 542.5732 Evaluate side-chains 307 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 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 A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain 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: 0.2980 chunk 66 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN O 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057482 restraints weight = 45537.962| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.30 r_work: 0.2906 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17433 Z= 0.226 Angle : 0.638 11.318 23718 Z= 0.320 Chirality : 0.043 0.162 2634 Planarity : 0.004 0.060 3000 Dihedral : 7.617 61.796 2781 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.64 % Allowed : 18.43 % Favored : 77.93 % 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: -0.10 (0.18), residues: 2127 helix: 1.00 (0.41), residues: 156 sheet: -0.01 (0.19), residues: 762 loop : -0.14 (0.18), residues: 1209 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 0.009 0.001 PHE I 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 0.00400 ( 6) link_NAG-ASN : angle 2.40967 ( 18) link_ALPHA1-6 : bond 0.00252 ( 3) link_ALPHA1-6 : angle 2.39254 ( 9) link_BETA1-4 : bond 0.00164 ( 6) link_BETA1-4 : angle 2.29024 ( 18) link_ALPHA1-3 : bond 0.00462 ( 6) link_ALPHA1-3 : angle 2.03358 ( 18) hydrogen bonds : bond 0.03716 ( 516) hydrogen bonds : angle 5.45129 ( 1410) SS BOND : bond 0.00339 ( 21) SS BOND : angle 0.46247 ( 42) covalent geometry : bond 0.00505 (17391) covalent geometry : angle 0.62823 (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 358 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8591 (mt0) cc_final: 0.8051 (mm-40) REVERT: F 56 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8190 (mmtm) REVERT: F 127 ASP cc_start: 0.8451 (p0) cc_final: 0.8032 (p0) REVERT: G 523 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7482 (tm-30) REVERT: H 41 PRO cc_start: 0.8376 (Cg_exo) cc_final: 0.8142 (Cg_endo) REVERT: H 90 ASP cc_start: 0.6658 (m-30) cc_final: 0.6432 (m-30) REVERT: I 6 GLU cc_start: 0.8118 (mp0) cc_final: 0.7591 (mp0) REVERT: I 46 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: I 85 MET cc_start: 0.8443 (mtt) cc_final: 0.8160 (mtt) REVERT: I 87 ASN cc_start: 0.8925 (t0) cc_final: 0.8657 (t0) REVERT: I 95 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: I 114 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7466 (mtm110) REVERT: I 117 LEU cc_start: 0.9147 (tt) cc_final: 0.8908 (tm) REVERT: J 16 GLN cc_start: 0.8036 (pt0) cc_final: 0.7688 (pt0) REVERT: J 51 TYR cc_start: 0.9019 (p90) cc_final: 0.8782 (p90) REVERT: J 87 ASP cc_start: 0.8874 (m-30) cc_final: 0.8549 (m-30) REVERT: J 96 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8439 (mtm-85) REVERT: J 98 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8204 (mpp80) REVERT: A 56 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8244 (mmtm) REVERT: B 523 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 551 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7336 (pp30) REVERT: C 13 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8714 (mmmm) REVERT: C 41 PRO cc_start: 0.8647 (Cg_exo) cc_final: 0.7958 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8061 (mm110) REVERT: C 46 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 54 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7267 (ttm110) REVERT: C 213 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8615 (mm) REVERT: D 25 SER cc_start: 0.8812 (m) cc_final: 0.8314 (p) REVERT: D 46 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: D 87 ASN cc_start: 0.8966 (t0) cc_final: 0.8710 (t0) REVERT: D 114 ARG cc_start: 0.7233 (mpt180) cc_final: 0.6873 (mpt180) REVERT: E 81 GLN cc_start: 0.8723 (mp10) cc_final: 0.8293 (mp10) REVERT: E 85 GLU cc_start: 0.8332 (tt0) cc_final: 0.8026 (tt0) REVERT: E 87 ASP cc_start: 0.8764 (m-30) cc_final: 0.8360 (m-30) REVERT: E 94 ASP cc_start: 0.8182 (t0) cc_final: 0.7897 (t70) REVERT: E 108 LYS cc_start: 0.8819 (tptm) cc_final: 0.8479 (tptp) REVERT: L 523 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7320 (tm-30) REVERT: L 545 GLU cc_start: 0.8549 (mp0) cc_final: 0.8259 (mp0) REVERT: M 41 PRO cc_start: 0.8643 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8408 (t0) cc_final: 0.8022 (t0) REVERT: N 6 GLU cc_start: 0.8066 (mp0) cc_final: 0.7607 (mp0) REVERT: N 46 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7562 (tm-30) REVERT: N 87 ASN cc_start: 0.8885 (t0) cc_final: 0.8634 (t0) REVERT: N 95 MET cc_start: 0.8597 (mtp) cc_final: 0.7719 (ttm) REVERT: N 114 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7690 (mtm110) REVERT: O 16 GLN cc_start: 0.8312 (pt0) cc_final: 0.7995 (pp30) REVERT: O 85 GLU cc_start: 0.8388 (tt0) cc_final: 0.8043 (tt0) REVERT: O 108 LYS cc_start: 0.8817 (tptm) cc_final: 0.8461 (tptp) outliers start: 65 outliers final: 33 residues processed: 324 average time/residue: 1.4666 time to fit residues: 523.5865 Evaluate side-chains 314 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 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 72 MET Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 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 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 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 2 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET 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: 3.9990 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.0570 chunk 181 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- 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** A 188 GLN ** 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 100 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 GLN N 86 ASN ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056759 restraints weight = 46143.058| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.33 r_work: 0.2897 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17433 Z= 0.250 Angle : 0.656 9.358 23718 Z= 0.332 Chirality : 0.044 0.159 2634 Planarity : 0.004 0.043 3000 Dihedral : 7.507 59.831 2781 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.59 % Allowed : 18.77 % Favored : 77.65 % 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: 867 loop : -0.17 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE N 70 TYR 0.028 0.001 TYR E 51 ARG 0.008 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 6) link_NAG-ASN : angle 2.49658 ( 18) link_ALPHA1-6 : bond 0.00388 ( 3) link_ALPHA1-6 : angle 2.39983 ( 9) link_BETA1-4 : bond 0.00131 ( 6) link_BETA1-4 : angle 2.34453 ( 18) link_ALPHA1-3 : bond 0.00424 ( 6) link_ALPHA1-3 : angle 1.93391 ( 18) hydrogen bonds : bond 0.03621 ( 516) hydrogen bonds : angle 5.39017 ( 1410) SS BOND : bond 0.00364 ( 21) SS BOND : angle 0.43438 ( 42) covalent geometry : bond 0.00560 (17391) covalent geometry : angle 0.64652 (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 360 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8609 (mt0) cc_final: 0.8097 (mm-40) REVERT: F 54 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8049 (ptm160) REVERT: F 56 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8215 (mmtm) REVERT: F 100 GLU cc_start: 0.8713 (mp0) cc_final: 0.8430 (mp0) REVERT: F 127 ASP cc_start: 0.8486 (p0) cc_final: 0.8062 (p0) REVERT: G 523 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7121 (tm-30) REVERT: H 40 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7968 (tpp80) REVERT: H 89 GLU cc_start: 0.8193 (pp20) cc_final: 0.7987 (pp20) REVERT: H 146 HIS cc_start: 0.7442 (m90) cc_final: 0.7180 (m90) REVERT: I 6 GLU cc_start: 0.8102 (mp0) cc_final: 0.7617 (mp0) REVERT: I 46 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: I 85 MET cc_start: 0.8436 (mtt) cc_final: 0.8200 (mtt) REVERT: I 87 ASN cc_start: 0.8963 (t0) cc_final: 0.8701 (t0) REVERT: I 95 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7700 (ttm) REVERT: I 114 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7524 (mtm110) REVERT: I 117 LEU cc_start: 0.9128 (tt) cc_final: 0.8889 (tm) REVERT: J 16 GLN cc_start: 0.8124 (pt0) cc_final: 0.7799 (pt0) REVERT: J 26 TYR cc_start: 0.9428 (p90) cc_final: 0.9077 (p90) REVERT: J 51 TYR cc_start: 0.9035 (p90) cc_final: 0.8789 (p90) REVERT: J 68 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8506 (tmmm) REVERT: J 87 ASP cc_start: 0.8874 (m-30) cc_final: 0.8180 (m-30) REVERT: J 96 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8376 (mtm-85) REVERT: J 98 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8245 (mpp80) REVERT: J 108 LYS cc_start: 0.8740 (tptp) cc_final: 0.8462 (tppt) REVERT: A 56 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8230 (mmtm) REVERT: A 112 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8551 (mt-10) REVERT: B 523 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 551 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7363 (pp30) REVERT: C 13 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8736 (mmmm) REVERT: C 41 PRO cc_start: 0.8763 (Cg_exo) cc_final: 0.8506 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8684 (mt-10) REVERT: C 54 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7200 (ttm110) REVERT: C 213 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8659 (mm) REVERT: D 25 SER cc_start: 0.8833 (m) cc_final: 0.8315 (p) REVERT: D 46 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: D 87 ASN cc_start: 0.9000 (t0) cc_final: 0.8748 (t0) REVERT: E 81 GLN cc_start: 0.8801 (mp10) cc_final: 0.8203 (mp10) REVERT: E 85 GLU cc_start: 0.8378 (tt0) cc_final: 0.8042 (tt0) REVERT: E 87 ASP cc_start: 0.8859 (m-30) cc_final: 0.8475 (m-30) REVERT: E 108 LYS cc_start: 0.8846 (tptm) cc_final: 0.8501 (tptp) REVERT: K 44 GLN cc_start: 0.8394 (mt0) cc_final: 0.7810 (mm-40) REVERT: L 523 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7377 (tm-30) REVERT: L 545 GLU cc_start: 0.8557 (mp0) cc_final: 0.8207 (mp0) REVERT: M 11 LEU cc_start: 0.8885 (tp) cc_final: 0.8680 (tp) REVERT: M 41 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8509 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8310 (t0) cc_final: 0.7985 (t0) REVERT: M 156 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8097 (ttp80) REVERT: N 6 GLU cc_start: 0.7976 (mp0) cc_final: 0.7657 (mp0) REVERT: N 46 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7572 (tm-30) REVERT: N 87 ASN cc_start: 0.9002 (t0) cc_final: 0.8741 (t0) REVERT: N 95 MET cc_start: 0.8635 (mtp) cc_final: 0.7588 (ttm) REVERT: N 114 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7748 (mtm110) REVERT: O 16 GLN cc_start: 0.8219 (pt0) cc_final: 0.7986 (pp30) REVERT: O 85 GLU cc_start: 0.8395 (tt0) cc_final: 0.8085 (tt0) REVERT: O 94 ASP cc_start: 0.8221 (t70) cc_final: 0.7614 (t70) REVERT: O 108 LYS cc_start: 0.8818 (tptm) cc_final: 0.8500 (tptp) outliers start: 64 outliers final: 34 residues processed: 328 average time/residue: 1.9202 time to fit residues: 695.8649 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 : 1.846 ------------------------------------------------------------------------------- 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 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 72 MET 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 D residue 110 ASP 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 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 586 ASN ** 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 L 586 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058456 restraints weight = 45976.600| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.23 r_work: 0.2958 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17433 Z= 0.146 Angle : 0.632 9.483 23718 Z= 0.316 Chirality : 0.043 0.180 2634 Planarity : 0.004 0.057 3000 Dihedral : 7.137 59.935 2781 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.14 % Allowed : 19.78 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.18), residues: 2127 helix: 1.21 (0.42), residues: 156 sheet: -0.01 (0.19), residues: 729 loop : -0.26 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.002 0.000 HIS H 35 PHE 0.007 0.001 PHE N 70 TYR 0.029 0.001 TYR E 51 ARG 0.009 0.001 ARG K 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 6) link_NAG-ASN : angle 2.20173 ( 18) link_ALPHA1-6 : bond 0.00052 ( 3) link_ALPHA1-6 : angle 2.06684 ( 9) link_BETA1-4 : bond 0.00449 ( 6) link_BETA1-4 : angle 2.25605 ( 18) link_ALPHA1-3 : bond 0.00717 ( 6) link_ALPHA1-3 : angle 1.76773 ( 18) hydrogen bonds : bond 0.03219 ( 516) hydrogen bonds : angle 5.23415 ( 1410) SS BOND : bond 0.00211 ( 21) SS BOND : angle 0.36026 ( 42) covalent geometry : bond 0.00328 (17391) covalent geometry : angle 0.62451 (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: 56 poor density : 301 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8624 (mt0) cc_final: 0.8119 (mm-40) REVERT: F 127 ASP cc_start: 0.8390 (p0) cc_final: 0.7940 (p0) REVERT: G 523 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7315 (tm-30) REVERT: H 89 GLU cc_start: 0.8258 (pp20) cc_final: 0.8029 (pp20) REVERT: H 90 ASP cc_start: 0.6834 (m-30) cc_final: 0.6603 (m-30) REVERT: H 146 HIS cc_start: 0.7378 (m90) cc_final: 0.7112 (m90) REVERT: H 156 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8295 (ttp80) REVERT: I 6 GLU cc_start: 0.8031 (mp0) cc_final: 0.7708 (mp0) REVERT: I 46 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: I 87 ASN cc_start: 0.8963 (t0) cc_final: 0.8725 (t0) REVERT: I 95 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7825 (ttm) REVERT: I 104 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8268 (mpp80) REVERT: I 114 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7634 (mtm110) REVERT: I 117 LEU cc_start: 0.9113 (tt) cc_final: 0.8879 (tm) REVERT: J 16 GLN cc_start: 0.7814 (pt0) cc_final: 0.7455 (pt0) REVERT: J 26 TYR cc_start: 0.9429 (p90) cc_final: 0.9103 (p90) REVERT: J 87 ASP cc_start: 0.8894 (m-30) cc_final: 0.8557 (m-30) REVERT: J 94 ASP cc_start: 0.8067 (t0) cc_final: 0.7810 (t70) REVERT: J 96 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8367 (mtm-85) REVERT: J 98 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8117 (mpp80) REVERT: A 56 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8230 (mmtm) REVERT: B 523 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 551 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7420 (pp30) REVERT: C 13 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8722 (mmmm) REVERT: C 34 MET cc_start: 0.9421 (mmm) cc_final: 0.9193 (tpt) REVERT: C 40 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7761 (tpp80) REVERT: C 41 PRO cc_start: 0.8748 (Cg_exo) cc_final: 0.7597 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8044 (mm110) REVERT: C 46 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8683 (mt-10) REVERT: C 54 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7246 (ttm170) REVERT: C 59 ASP cc_start: 0.8308 (t0) cc_final: 0.8081 (t0) REVERT: C 89 GLU cc_start: 0.8190 (pp20) cc_final: 0.7898 (pp20) REVERT: C 213 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 25 SER cc_start: 0.8825 (m) cc_final: 0.8315 (p) REVERT: D 46 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: D 87 ASN cc_start: 0.9035 (t0) cc_final: 0.8834 (t0) REVERT: D 95 MET cc_start: 0.8290 (mtp) cc_final: 0.7578 (ttm) REVERT: E 81 GLN cc_start: 0.8863 (mp10) cc_final: 0.8423 (mp10) REVERT: E 85 GLU cc_start: 0.8363 (tt0) cc_final: 0.8101 (tt0) REVERT: E 87 ASP cc_start: 0.8797 (m-30) cc_final: 0.8420 (m-30) REVERT: E 94 ASP cc_start: 0.8029 (t0) cc_final: 0.7809 (t70) REVERT: E 108 LYS cc_start: 0.8898 (tptm) cc_final: 0.8565 (tptp) REVERT: K 44 GLN cc_start: 0.8443 (mt0) cc_final: 0.7851 (mm-40) REVERT: K 77 THR cc_start: 0.8877 (p) cc_final: 0.8603 (t) REVERT: L 523 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7305 (tm-30) REVERT: L 545 GLU cc_start: 0.8528 (mp0) cc_final: 0.8202 (mp0) REVERT: M 11 LEU cc_start: 0.8870 (tp) cc_final: 0.8597 (tp) REVERT: M 59 ASP cc_start: 0.8257 (t0) cc_final: 0.7949 (t0) REVERT: M 89 GLU cc_start: 0.8012 (pp20) cc_final: 0.7651 (pp20) REVERT: M 156 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8279 (ttp80) REVERT: N 6 GLU cc_start: 0.7913 (mp0) cc_final: 0.7686 (mp0) REVERT: N 46 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7581 (tm-30) REVERT: N 87 ASN cc_start: 0.8975 (t0) cc_final: 0.8749 (t0) REVERT: N 95 MET cc_start: 0.8671 (mtp) cc_final: 0.7729 (ttm) REVERT: N 114 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7813 (mtm110) REVERT: O 16 GLN cc_start: 0.8063 (pt0) cc_final: 0.7837 (pp30) REVERT: O 85 GLU cc_start: 0.8382 (tt0) cc_final: 0.8084 (tt0) REVERT: O 94 ASP cc_start: 0.8140 (t70) cc_final: 0.7632 (t70) REVERT: O 96 ARG cc_start: 0.9009 (mpp80) cc_final: 0.8684 (mpp80) REVERT: O 108 LYS cc_start: 0.8840 (tptm) cc_final: 0.8520 (tptp) outliers start: 56 outliers final: 28 residues processed: 328 average time/residue: 1.6063 time to fit residues: 580.4965 Evaluate side-chains 321 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 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 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 110 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain 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 232 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP 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: 0.0050 chunk 206 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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** D 103 GLN E 28 ASN L 551 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058611 restraints weight = 45590.680| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.23 r_work: 0.2958 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17433 Z= 0.147 Angle : 0.636 8.720 23718 Z= 0.317 Chirality : 0.043 0.165 2634 Planarity : 0.004 0.045 3000 Dihedral : 6.884 58.808 2781 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.08 % Allowed : 20.78 % Favored : 76.13 % 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: -0.19 (0.18), residues: 2127 helix: 1.34 (0.43), residues: 156 sheet: -0.11 (0.19), residues: 753 loop : -0.24 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE N 70 TYR 0.029 0.001 TYR E 51 ARG 0.008 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 6) link_NAG-ASN : angle 2.10527 ( 18) link_ALPHA1-6 : bond 0.00028 ( 3) link_ALPHA1-6 : angle 2.01167 ( 9) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 2.30252 ( 18) link_ALPHA1-3 : bond 0.00688 ( 6) link_ALPHA1-3 : angle 1.84020 ( 18) hydrogen bonds : bond 0.03113 ( 516) hydrogen bonds : angle 5.08995 ( 1410) SS BOND : bond 0.00204 ( 21) SS BOND : angle 0.31940 ( 42) covalent geometry : bond 0.00330 (17391) covalent geometry : angle 0.62808 (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 356 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8587 (mt0) cc_final: 0.8051 (mm-40) REVERT: F 54 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8008 (ptm-80) REVERT: F 56 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8183 (mmtm) REVERT: F 127 ASP cc_start: 0.8387 (p0) cc_final: 0.7949 (p0) REVERT: G 523 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7172 (tm-30) REVERT: H 90 ASP cc_start: 0.6733 (m-30) cc_final: 0.6458 (m-30) REVERT: H 146 HIS cc_start: 0.7467 (m90) cc_final: 0.7187 (m90) REVERT: I 6 GLU cc_start: 0.7910 (mp0) cc_final: 0.7580 (mp0) REVERT: I 43 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8268 (mtpp) REVERT: I 46 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: I 87 ASN cc_start: 0.8937 (t0) cc_final: 0.8729 (t0) REVERT: I 95 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7821 (ttm) REVERT: I 114 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7611 (mtm110) REVERT: I 117 LEU cc_start: 0.9101 (tt) cc_final: 0.8853 (tm) REVERT: J 16 GLN cc_start: 0.7874 (pt0) cc_final: 0.7522 (pt0) REVERT: J 87 ASP cc_start: 0.8859 (m-30) cc_final: 0.8552 (m-30) REVERT: J 94 ASP cc_start: 0.8052 (t0) cc_final: 0.7795 (t70) REVERT: J 96 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8445 (mtm-85) REVERT: J 98 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8117 (mpp80) REVERT: A 56 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8232 (mmtm) REVERT: B 523 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7268 (tm-30) REVERT: B 551 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7273 (pp30) REVERT: C 13 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8724 (mmmm) REVERT: C 34 MET cc_start: 0.9419 (mmm) cc_final: 0.9203 (tpt) REVERT: C 40 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7839 (tpp80) REVERT: C 41 PRO cc_start: 0.8739 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7994 (mm110) REVERT: C 46 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 54 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: C 89 GLU cc_start: 0.8204 (pp20) cc_final: 0.7898 (pp20) REVERT: C 139 ASP cc_start: 0.8667 (p0) cc_final: 0.8169 (p0) REVERT: C 213 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8593 (mm) REVERT: D 25 SER cc_start: 0.8777 (m) cc_final: 0.8237 (p) REVERT: D 39 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 46 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: D 95 MET cc_start: 0.8302 (mtp) cc_final: 0.7546 (ttm) REVERT: E 68 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8153 (tmmm) REVERT: E 81 GLN cc_start: 0.8815 (mp10) cc_final: 0.8215 (mp10) REVERT: E 85 GLU cc_start: 0.8364 (tt0) cc_final: 0.8117 (tt0) REVERT: E 94 ASP cc_start: 0.8021 (t0) cc_final: 0.7802 (t70) REVERT: E 98 ARG cc_start: 0.8433 (mpp80) cc_final: 0.8201 (mpp80) REVERT: E 108 LYS cc_start: 0.8903 (tptm) cc_final: 0.8546 (tptp) REVERT: E 109 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8303 (tp) REVERT: K 44 GLN cc_start: 0.8449 (mt0) cc_final: 0.7884 (mm-40) REVERT: K 77 THR cc_start: 0.8833 (p) cc_final: 0.8594 (t) REVERT: L 522 ASP cc_start: 0.7542 (t70) cc_final: 0.7167 (t0) REVERT: L 523 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7447 (tm-30) REVERT: L 545 GLU cc_start: 0.8500 (mp0) cc_final: 0.8183 (mp0) REVERT: M 11 LEU cc_start: 0.8845 (tp) cc_final: 0.8637 (tp) REVERT: M 59 ASP cc_start: 0.8225 (t0) cc_final: 0.7914 (t0) REVERT: M 156 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8267 (ttp80) REVERT: N 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7634 (mp0) REVERT: N 39 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8465 (tm-30) REVERT: N 46 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7589 (tm-30) REVERT: N 71 THR cc_start: 0.9302 (m) cc_final: 0.9097 (t) REVERT: N 85 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8215 (mtt) REVERT: N 95 MET cc_start: 0.8646 (mtp) cc_final: 0.7637 (ttm) REVERT: N 114 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7844 (mtm110) REVERT: O 16 GLN cc_start: 0.8001 (pt0) cc_final: 0.7772 (pp30) REVERT: O 85 GLU cc_start: 0.8394 (tt0) cc_final: 0.8035 (tt0) REVERT: O 94 ASP cc_start: 0.8116 (t70) cc_final: 0.7638 (t70) REVERT: O 108 LYS cc_start: 0.8831 (tptm) cc_final: 0.8518 (tptp) outliers start: 55 outliers final: 31 residues processed: 332 average time/residue: 1.5222 time to fit residues: 556.2032 Evaluate side-chains 327 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 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 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 232 THR Chi-restraints excluded: chain N residue 61 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** D 103 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058727 restraints weight = 45503.411| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.24 r_work: 0.2962 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17433 Z= 0.144 Angle : 0.648 8.744 23718 Z= 0.325 Chirality : 0.043 0.176 2634 Planarity : 0.004 0.046 3000 Dihedral : 6.753 57.948 2781 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.86 % Allowed : 22.13 % Favored : 75.01 % 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: -0.15 (0.18), residues: 2127 helix: 1.38 (0.43), residues: 156 sheet: -0.04 (0.19), residues: 732 loop : -0.25 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.002 0.000 HIS H 35 PHE 0.013 0.001 PHE N 70 TYR 0.031 0.001 TYR J 51 ARG 0.010 0.001 ARG H 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 6) link_NAG-ASN : angle 2.01269 ( 18) link_ALPHA1-6 : bond 0.00056 ( 3) link_ALPHA1-6 : angle 1.96122 ( 9) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 2.38218 ( 18) link_ALPHA1-3 : bond 0.00719 ( 6) link_ALPHA1-3 : angle 1.81906 ( 18) hydrogen bonds : bond 0.03058 ( 516) hydrogen bonds : angle 4.99349 ( 1410) SS BOND : bond 0.00179 ( 21) SS BOND : angle 0.86153 ( 42) covalent geometry : bond 0.00324 (17391) covalent geometry : angle 0.63984 (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 347 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8600 (mt0) cc_final: 0.8058 (mm-40) REVERT: F 56 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8189 (mmtm) REVERT: F 127 ASP cc_start: 0.8407 (p0) cc_final: 0.7977 (p0) REVERT: G 523 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7157 (tm-30) REVERT: G 551 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: H 80 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: H 146 HIS cc_start: 0.7475 (m90) cc_final: 0.7200 (m90) REVERT: I 6 GLU cc_start: 0.7802 (mp0) cc_final: 0.7521 (mp0) REVERT: I 39 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8281 (tm-30) REVERT: I 43 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8349 (mtpp) REVERT: I 46 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: I 85 MET cc_start: 0.8467 (mpp) cc_final: 0.8211 (mpp) REVERT: I 95 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7819 (ttm) REVERT: I 114 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7650 (mtm110) REVERT: I 117 LEU cc_start: 0.9066 (tt) cc_final: 0.8808 (tm) REVERT: J 16 GLN cc_start: 0.7845 (pt0) cc_final: 0.7497 (pt0) REVERT: J 87 ASP cc_start: 0.8892 (m-30) cc_final: 0.8552 (m-30) REVERT: J 94 ASP cc_start: 0.8111 (t0) cc_final: 0.7848 (t70) REVERT: J 96 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8409 (mtm-85) REVERT: J 98 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8090 (mpp80) REVERT: A 56 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8230 (mmtm) REVERT: B 523 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 551 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7280 (pp30) REVERT: C 13 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8731 (mmmm) REVERT: C 34 MET cc_start: 0.9449 (mmm) cc_final: 0.9219 (tpt) REVERT: C 40 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7795 (tpp80) REVERT: C 41 PRO cc_start: 0.8737 (Cg_exo) cc_final: 0.7718 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7999 (mm110) REVERT: C 46 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8667 (mt-10) REVERT: C 54 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.6665 (tpp80) REVERT: C 59 ASP cc_start: 0.8300 (t0) cc_final: 0.8060 (t0) REVERT: C 62 GLU cc_start: 0.8492 (pt0) cc_final: 0.8126 (pm20) REVERT: C 89 GLU cc_start: 0.8203 (pp20) cc_final: 0.7893 (pp20) REVERT: C 139 ASP cc_start: 0.8715 (p0) cc_final: 0.8214 (p0) REVERT: C 213 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 25 SER cc_start: 0.8766 (m) cc_final: 0.8227 (p) REVERT: D 39 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 46 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: D 95 MET cc_start: 0.8371 (mtp) cc_final: 0.7594 (ttm) REVERT: E 68 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8149 (tmmm) REVERT: E 81 GLN cc_start: 0.8819 (mp10) cc_final: 0.8209 (mp10) REVERT: E 94 ASP cc_start: 0.8039 (t0) cc_final: 0.7828 (t70) REVERT: E 108 LYS cc_start: 0.8913 (tptm) cc_final: 0.8607 (tptp) REVERT: E 109 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8456 (tp) REVERT: L 523 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7333 (tm-30) REVERT: L 545 GLU cc_start: 0.8509 (mp0) cc_final: 0.8192 (mp0) REVERT: M 11 LEU cc_start: 0.8905 (tp) cc_final: 0.8695 (tp) REVERT: M 59 ASP cc_start: 0.8169 (t0) cc_final: 0.7925 (t0) REVERT: M 156 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8265 (ttp80) REVERT: N 6 GLU cc_start: 0.7828 (mp0) cc_final: 0.7550 (mp0) REVERT: N 39 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8464 (tm-30) REVERT: N 46 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7619 (tm-30) REVERT: N 85 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8174 (mtt) REVERT: N 95 MET cc_start: 0.8640 (mtp) cc_final: 0.7683 (ttm) REVERT: N 114 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7843 (mtm110) REVERT: O 16 GLN cc_start: 0.8056 (pt0) cc_final: 0.7822 (pp30) REVERT: O 85 GLU cc_start: 0.8377 (tt0) cc_final: 0.8011 (tt0) REVERT: O 96 ARG cc_start: 0.8991 (mpp80) cc_final: 0.8733 (mpp80) REVERT: O 108 LYS cc_start: 0.8841 (tptm) cc_final: 0.8513 (tptp) outliers start: 51 outliers final: 32 residues processed: 322 average time/residue: 1.5478 time to fit residues: 548.0769 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 34 ASP Chi-restraints excluded: chain E residue 41 LEU 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 L residue 566 THR 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 232 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 85 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 185 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 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: 1.2702 ------------------------------------------------------------------------------- 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** D 103 GLN E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057838 restraints weight = 45984.324| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.34 r_work: 0.2929 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3593 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= 0.203 Angle : 0.680 9.158 23718 Z= 0.343 Chirality : 0.043 0.173 2634 Planarity : 0.004 0.045 3000 Dihedral : 6.782 57.367 2781 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.91 % Allowed : 22.58 % 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: -0.17 (0.18), residues: 2127 helix: 1.46 (0.43), residues: 156 sheet: -0.13 (0.19), residues: 783 loop : -0.21 (0.18), residues: 1188 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 0.016 0.001 PHE N 70 TYR 0.028 0.001 TYR E 51 ARG 0.009 0.001 ARG F 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 6) link_NAG-ASN : angle 2.17219 ( 18) link_ALPHA1-6 : bond 0.00204 ( 3) link_ALPHA1-6 : angle 2.15958 ( 9) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 2.52935 ( 18) link_ALPHA1-3 : bond 0.00579 ( 6) link_ALPHA1-3 : angle 1.91716 ( 18) hydrogen bonds : bond 0.03204 ( 516) hydrogen bonds : angle 5.02978 ( 1410) SS BOND : bond 0.00267 ( 21) SS BOND : angle 0.78322 ( 42) covalent geometry : bond 0.00460 (17391) covalent geometry : angle 0.67098 (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: 52 poor density : 289 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8559 (mt0) cc_final: 0.8004 (mm-40) REVERT: F 54 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8042 (ptm-80) REVERT: F 56 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8177 (mmtm) REVERT: F 127 ASP cc_start: 0.8460 (p0) cc_final: 0.8042 (p0) REVERT: G 523 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7185 (tm-30) REVERT: G 545 GLU cc_start: 0.7914 (pp20) cc_final: 0.7558 (tm-30) REVERT: G 551 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7635 (pp30) REVERT: H 80 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: H 146 HIS cc_start: 0.7488 (m90) cc_final: 0.7200 (m90) REVERT: H 156 ARG cc_start: 0.8861 (tmt90) cc_final: 0.8518 (ttp80) REVERT: I 6 GLU cc_start: 0.7863 (mp0) cc_final: 0.7505 (mp0) REVERT: I 43 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8224 (mtpp) REVERT: I 46 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: I 95 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: I 104 ARG cc_start: 0.8459 (mpp-170) cc_final: 0.8215 (mpt-90) REVERT: I 114 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7602 (mtm110) REVERT: I 117 LEU cc_start: 0.9055 (tt) cc_final: 0.8779 (tm) REVERT: J 16 GLN cc_start: 0.7993 (pt0) cc_final: 0.7734 (pt0) REVERT: J 87 ASP cc_start: 0.8837 (m-30) cc_final: 0.8506 (m-30) REVERT: J 94 ASP cc_start: 0.8096 (t0) cc_final: 0.7846 (t70) REVERT: J 96 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8348 (mtm-85) REVERT: J 98 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8141 (mpp80) REVERT: A 56 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8181 (mmtm) REVERT: B 523 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 551 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7354 (pp30) REVERT: C 13 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8738 (mmmm) REVERT: C 34 MET cc_start: 0.9440 (mmm) cc_final: 0.9199 (tpt) REVERT: C 41 PRO cc_start: 0.8816 (Cg_exo) cc_final: 0.8285 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8041 (mm110) REVERT: C 46 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8685 (mt-10) REVERT: C 59 ASP cc_start: 0.8380 (t0) cc_final: 0.8097 (t0) REVERT: C 62 GLU cc_start: 0.8525 (pt0) cc_final: 0.8140 (pm20) REVERT: C 89 GLU cc_start: 0.8227 (pp20) cc_final: 0.7971 (pp20) REVERT: C 139 ASP cc_start: 0.8729 (p0) cc_final: 0.8236 (p0) REVERT: C 213 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8580 (mm) REVERT: D 25 SER cc_start: 0.8785 (m) cc_final: 0.8279 (p) REVERT: D 39 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 46 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: D 95 MET cc_start: 0.8312 (mtp) cc_final: 0.7349 (ttm) REVERT: D 114 ARG cc_start: 0.6866 (mpt180) cc_final: 0.6555 (mpt180) REVERT: E 52 ASP cc_start: 0.8507 (t0) cc_final: 0.8264 (t0) REVERT: E 81 GLN cc_start: 0.8743 (mp10) cc_final: 0.8258 (mp10) REVERT: E 94 ASP cc_start: 0.8103 (t0) cc_final: 0.7874 (t70) REVERT: E 108 LYS cc_start: 0.8857 (tptm) cc_final: 0.8560 (tptp) REVERT: E 109 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8528 (tp) REVERT: K 50 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6793 (mmmt) REVERT: L 523 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7331 (tm-30) REVERT: L 545 GLU cc_start: 0.8526 (mp0) cc_final: 0.8175 (mp0) REVERT: M 11 LEU cc_start: 0.8885 (tp) cc_final: 0.8670 (tp) REVERT: M 59 ASP cc_start: 0.8189 (t0) cc_final: 0.7901 (t0) REVERT: M 80 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: M 156 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8255 (ttp80) REVERT: N 6 GLU cc_start: 0.7816 (mp0) cc_final: 0.7477 (mp0) REVERT: N 39 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8452 (tm-30) REVERT: N 46 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7579 (tm-30) REVERT: N 75 ASP cc_start: 0.8796 (t0) cc_final: 0.8587 (t0) REVERT: N 85 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: N 95 MET cc_start: 0.8601 (mtp) cc_final: 0.7581 (ttm) REVERT: N 114 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7778 (mtm110) REVERT: O 16 GLN cc_start: 0.8110 (pt0) cc_final: 0.7891 (pp30) REVERT: O 85 GLU cc_start: 0.8403 (tt0) cc_final: 0.7974 (tt0) REVERT: O 94 ASP cc_start: 0.8228 (t70) cc_final: 0.7678 (t70) REVERT: O 96 ARG cc_start: 0.8973 (mpp80) cc_final: 0.8594 (mpp80) REVERT: O 108 LYS cc_start: 0.8817 (tptm) cc_final: 0.8484 (tptp) outliers start: 52 outliers final: 29 residues processed: 320 average time/residue: 1.7079 time to fit residues: 604.4631 Evaluate side-chains 322 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 551 GLN Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 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 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 E residue 34 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 566 THR 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 232 THR Chi-restraints excluded: chain N residue 61 ASP 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 14 optimal weight: 0.0870 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.077477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058100 restraints weight = 46037.742| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.33 r_work: 0.2937 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17433 Z= 0.172 Angle : 0.679 9.912 23718 Z= 0.341 Chirality : 0.043 0.167 2634 Planarity : 0.004 0.046 3000 Dihedral : 6.653 56.737 2781 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.52 % Allowed : 23.08 % Favored : 74.40 % 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: -0.19 (0.18), residues: 2127 helix: 1.46 (0.42), residues: 156 sheet: -0.14 (0.19), residues: 783 loop : -0.24 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE N 70 TYR 0.031 0.001 TYR J 51 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 6) link_NAG-ASN : angle 2.13448 ( 18) link_ALPHA1-6 : bond 0.00088 ( 3) link_ALPHA1-6 : angle 2.05882 ( 9) link_BETA1-4 : bond 0.00363 ( 6) link_BETA1-4 : angle 2.53094 ( 18) link_ALPHA1-3 : bond 0.00667 ( 6) link_ALPHA1-3 : angle 1.82997 ( 18) hydrogen bonds : bond 0.03101 ( 516) hydrogen bonds : angle 5.01956 ( 1410) SS BOND : bond 0.00226 ( 21) SS BOND : angle 0.64085 ( 42) covalent geometry : bond 0.00390 (17391) covalent geometry : angle 0.67090 (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 337 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8618 (mt0) cc_final: 0.8066 (mm-40) REVERT: F 56 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8186 (mmtm) REVERT: F 127 ASP cc_start: 0.8469 (p0) cc_final: 0.8053 (p0) REVERT: G 523 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7269 (tm-30) REVERT: G 545 GLU cc_start: 0.7819 (pp20) cc_final: 0.7478 (tm-30) REVERT: G 551 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: H 80 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: H 146 HIS cc_start: 0.7481 (m90) cc_final: 0.7194 (m90) REVERT: H 156 ARG cc_start: 0.8854 (tmt90) cc_final: 0.8517 (ttp80) REVERT: I 6 GLU cc_start: 0.7750 (mp0) cc_final: 0.7393 (mp0) REVERT: I 39 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8281 (tm-30) REVERT: I 43 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8327 (mtpp) REVERT: I 46 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: I 85 MET cc_start: 0.8354 (mpp) cc_final: 0.7862 (mpp) REVERT: I 95 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7743 (ttm) REVERT: I 104 ARG cc_start: 0.8492 (mpp-170) cc_final: 0.8248 (mpt-90) REVERT: I 114 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7611 (mtm110) REVERT: I 117 LEU cc_start: 0.9053 (tt) cc_final: 0.8774 (tm) REVERT: J 16 GLN cc_start: 0.7962 (pt0) cc_final: 0.7708 (pt0) REVERT: J 47 LYS cc_start: 0.9070 (tttp) cc_final: 0.8835 (tttt) REVERT: J 87 ASP cc_start: 0.8852 (m-30) cc_final: 0.8531 (m-30) REVERT: J 94 ASP cc_start: 0.8108 (t0) cc_final: 0.7878 (t70) REVERT: J 96 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8362 (mtm-85) REVERT: J 98 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8121 (mpp80) REVERT: A 56 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8218 (mmtm) REVERT: A 156 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8511 (mm-30) REVERT: B 523 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 551 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7313 (pp30) REVERT: C 13 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8749 (mmmm) REVERT: C 34 MET cc_start: 0.9444 (mmm) cc_final: 0.9211 (tpt) REVERT: C 40 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7801 (tpp80) REVERT: C 41 PRO cc_start: 0.8767 (Cg_exo) cc_final: 0.7581 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8059 (mm110) REVERT: C 54 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7089 (ttm110) REVERT: C 59 ASP cc_start: 0.8494 (t0) cc_final: 0.8149 (t0) REVERT: C 62 GLU cc_start: 0.8553 (pt0) cc_final: 0.8136 (pm20) REVERT: C 139 ASP cc_start: 0.8747 (p0) cc_final: 0.8261 (p0) REVERT: C 213 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8576 (mm) REVERT: D 25 SER cc_start: 0.8787 (m) cc_final: 0.8313 (p) REVERT: D 39 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8391 (tm-30) REVERT: D 46 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: D 67 ARG cc_start: 0.7871 (pmt-80) cc_final: 0.7061 (tpp80) REVERT: D 95 MET cc_start: 0.8349 (mtp) cc_final: 0.7423 (ttm) REVERT: D 114 ARG cc_start: 0.6997 (mpt180) cc_final: 0.6598 (mpt180) REVERT: E 52 ASP cc_start: 0.8457 (t0) cc_final: 0.8218 (t0) REVERT: E 68 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8155 (tmmm) REVERT: E 81 GLN cc_start: 0.8748 (mp10) cc_final: 0.8525 (mp10) REVERT: E 94 ASP cc_start: 0.8076 (t0) cc_final: 0.7853 (t70) REVERT: E 108 LYS cc_start: 0.8859 (tptm) cc_final: 0.8584 (tptp) REVERT: K 50 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6744 (mmmt) REVERT: L 523 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7306 (tm-30) REVERT: L 545 GLU cc_start: 0.8494 (mp0) cc_final: 0.8153 (mp0) REVERT: M 11 LEU cc_start: 0.8880 (tp) cc_final: 0.8666 (tp) REVERT: M 43 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8278 (mm110) REVERT: M 54 ARG cc_start: 0.7844 (ttt180) cc_final: 0.7154 (ttm170) REVERT: M 59 ASP cc_start: 0.8206 (t0) cc_final: 0.7928 (t0) REVERT: M 156 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8258 (ttp80) REVERT: N 6 GLU cc_start: 0.7782 (mp0) cc_final: 0.7471 (mp0) REVERT: N 39 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 46 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7599 (tm-30) REVERT: N 85 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: N 95 MET cc_start: 0.8602 (mtp) cc_final: 0.7566 (ttm) REVERT: N 114 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7797 (mtm110) REVERT: O 16 GLN cc_start: 0.8136 (pt0) cc_final: 0.7896 (pp30) REVERT: O 85 GLU cc_start: 0.8416 (tt0) cc_final: 0.8046 (tt0) REVERT: O 94 ASP cc_start: 0.8214 (t70) cc_final: 0.7714 (t70) REVERT: O 96 ARG cc_start: 0.8932 (mpp80) cc_final: 0.8571 (mpp80) REVERT: O 108 LYS cc_start: 0.8823 (tptm) cc_final: 0.8492 (tptp) outliers start: 45 outliers final: 29 residues processed: 320 average time/residue: 1.5459 time to fit residues: 545.0071 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 : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 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 E residue 34 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 61 ASP 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: 5.9990 chunk 32 optimal weight: 0.0060 chunk 130 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 156 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.077598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058189 restraints weight = 45826.465| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.33 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17433 Z= 0.183 Angle : 0.693 10.068 23718 Z= 0.348 Chirality : 0.043 0.170 2634 Planarity : 0.004 0.045 3000 Dihedral : 6.564 56.372 2779 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.75 % Allowed : 23.19 % 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: -0.22 (0.18), residues: 2127 helix: 1.41 (0.42), residues: 156 sheet: -0.14 (0.19), residues: 783 loop : -0.27 (0.18), residues: 1188 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 0.030 0.001 TYR E 51 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 6) link_NAG-ASN : angle 2.14449 ( 18) link_ALPHA1-6 : bond 0.00115 ( 3) link_ALPHA1-6 : angle 2.07386 ( 9) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 2.56152 ( 18) link_ALPHA1-3 : bond 0.00646 ( 6) link_ALPHA1-3 : angle 1.85344 ( 18) hydrogen bonds : bond 0.03148 ( 516) hydrogen bonds : angle 5.02430 ( 1410) SS BOND : bond 0.00227 ( 21) SS BOND : angle 0.64057 ( 42) covalent geometry : bond 0.00415 (17391) covalent geometry : angle 0.68475 (23613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13636.78 seconds wall clock time: 238 minutes 30.09 seconds (14310.09 seconds total)