Starting phenix.real_space_refine on Fri Jan 24 07:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpm_27638/01_2025/8dpm_27638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpm_27638/01_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_27638/01_2025/8dpm_27638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpm_27638/01_2025/8dpm_27638.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpm_27638/01_2025/8dpm_27638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpm_27638/01_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.15, per 1000 atoms: 0.60 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: 4.56 Conformation dependent library (CDL) restraints added in 2.2 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: 2.75 Creating SS restraints... Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 552 through 576 removed outlier: 3.636A pdb=" N CYS G 556 " --> pdb=" O ASP G 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN G 567 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU J 85 " --> pdb=" O THR J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'B' and resid 552 through 576 removed outlier: 3.644A pdb=" N CYS B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.905A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'L' and resid 552 through 576 removed outlier: 3.642A pdb=" N CYS L 556 " --> pdb=" O ASP L 552 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN L 567 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA L 568 " --> pdb=" O GLU L 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 571 " --> pdb=" O GLN L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 597 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP O 84 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN F 69 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 96 " --> pdb=" O THR G 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'F' and resid 108 through 114 removed outlier: 6.816A pdb=" N CYS F 108 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 141 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN F 110 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY F 143 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU F 112 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 138 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR F 220 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 140 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA F 222 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER F 142 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.694A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.627A pdb=" N VAL H 157 " --> pdb=" O ILE H 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 183 through 186 removed outlier: 6.682A pdb=" N TRP H 173 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 223 " --> pdb=" O GLN H 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.874A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 37 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 102 through 104 Processing sheet with id=AB4, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP J 87 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC1, first strand: chain 'A' and resid 108 through 114 removed outlier: 6.827A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.689A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.973A pdb=" N GLY C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.636A pdb=" N VAL C 157 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 186 removed outlier: 6.676A pdb=" N TRP C 173 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 223 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.860A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 37 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 87 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN K 69 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 96 " --> pdb=" O THR L 581 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 86 through 89 Processing sheet with id=AD6, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY K 143 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL K 138 " --> pdb=" O ILE K 218 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR K 220 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS K 140 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA K 222 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER K 142 " --> pdb=" O ALA K 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.697A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR M 107 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 142 through 144 removed outlier: 3.632A pdb=" N VAL M 157 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 183 through 186 removed outlier: 6.684A pdb=" N TRP M 173 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 223 " --> pdb=" O GLN M 176 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AE5, first strand: chain 'N' and resid 60 through 62 removed outlier: 6.867A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET N 34 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL N 37 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 102 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP O 87 " --> pdb=" O HIS O 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 18 through 23 556 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 5.24 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: 0.12 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.570 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- 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 17391 Z= 0.162 Angle : 0.495 6.514 23613 Z= 0.252 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 *********************** 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 : 1.910 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: 1.4310 time to fit residues: 755.2064 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 : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain M residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS H 110 GLN J 16 GLN J 28 ASN A 39 HIS B 521 GLN E 16 GLN E 28 ASN E 55 HIS K 39 HIS K 188 GLN L 521 GLN M 52 ASN N 103 GLN O 28 ASN O 100 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056224 restraints weight = 46403.912| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.32 r_work: 0.2872 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 17391 Z= 0.589 Angle : 0.752 8.376 23613 Z= 0.386 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8568 (mt0) cc_final: 0.7938 (mm-40) REVERT: F 54 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (ptm160) REVERT: F 100 GLU cc_start: 0.8668 (mp0) cc_final: 0.8413 (mp0) REVERT: F 136 ARG cc_start: 0.8465 (tpt90) cc_final: 0.8013 (tmt-80) REVERT: G 523 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7143 (tm-30) REVERT: I 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7389 (mp0) REVERT: I 46 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 67 ARG cc_start: 0.6848 (tpp-160) cc_final: 0.6648 (tpp-160) REVERT: I 117 LEU cc_start: 0.9073 (tt) cc_final: 0.8844 (tm) REVERT: J 16 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: J 26 TYR cc_start: 0.9455 (p90) cc_final: 0.9138 (p90) REVERT: J 44 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8719 (p) REVERT: J 83 GLU cc_start: 0.8755 (pt0) cc_final: 0.8504 (pm20) REVERT: J 96 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8357 (mtm-85) REVERT: A 56 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8208 (mmtm) REVERT: A 114 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (mtpp) REVERT: B 523 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 551 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7422 (pp30) REVERT: C 80 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6891 (p90) REVERT: C 213 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8752 (mm) REVERT: D 25 SER cc_start: 0.8966 (m) cc_final: 0.8325 (p) REVERT: D 43 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8279 (mmmm) REVERT: D 46 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 75 ASP cc_start: 0.8732 (t0) cc_final: 0.8412 (p0) REVERT: D 80 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8722 (mtpm) REVERT: D 87 ASN cc_start: 0.8908 (t0) cc_final: 0.8697 (t0) REVERT: D 110 ASP cc_start: 0.7895 (m-30) cc_final: 0.7677 (m-30) REVERT: E 85 GLU cc_start: 0.8306 (tt0) cc_final: 0.8077 (tt0) REVERT: E 87 ASP cc_start: 0.8774 (m-30) cc_final: 0.8443 (m-30) REVERT: K 54 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7903 (ptm160) REVERT: L 523 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7299 (tm-30) REVERT: L 545 GLU cc_start: 0.8546 (mp0) cc_final: 0.8307 (mp0) REVERT: M 59 ASP cc_start: 0.8450 (t0) cc_final: 0.7997 (t0) REVERT: M 156 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8316 (ttp80) REVERT: N 28 THR cc_start: 0.8800 (m) cc_final: 0.8498 (t) REVERT: N 43 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8484 (mmmm) REVERT: N 46 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7533 (tm-30) REVERT: N 61 ASP cc_start: 0.8032 (t0) cc_final: 0.7741 (t0) REVERT: N 67 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6562 (tpp-160) REVERT: N 95 MET cc_start: 0.8531 (mtp) cc_final: 0.7646 (ttm) REVERT: O 16 GLN cc_start: 0.8380 (pt0) cc_final: 0.8121 (pp30) REVERT: O 44 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8654 (p) REVERT: O 85 GLU cc_start: 0.8431 (tt0) cc_final: 0.8093 (tt0) REVERT: O 108 LYS cc_start: 0.8774 (tptm) cc_final: 0.8374 (tptp) outliers start: 78 outliers final: 31 residues processed: 348 average time/residue: 1.4896 time to fit residues: 570.9924 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 : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 189 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 516 HIS J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058918 restraints weight = 45735.778| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.23 r_work: 0.2959 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17391 Z= 0.227 Angle : 0.614 7.786 23613 Z= 0.311 Chirality : 0.043 0.158 2634 Planarity : 0.004 0.033 3000 Dihedral : 7.768 65.623 2781 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.36 % Allowed : 17.93 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2127 helix: 0.73 (0.42), residues: 156 sheet: 0.14 (0.19), residues: 741 loop : -0.11 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE N 70 TYR 0.026 0.001 TYR J 51 ARG 0.008 0.001 ARG N 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8583 (mt0) cc_final: 0.7970 (mm-40) REVERT: F 100 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: F 127 ASP cc_start: 0.8288 (p0) cc_final: 0.7870 (p0) REVERT: G 523 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7267 (tm-30) REVERT: I 6 GLU cc_start: 0.8076 (mp0) cc_final: 0.7712 (mp0) REVERT: I 43 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8309 (tttm) REVERT: I 46 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: I 87 ASN cc_start: 0.8925 (t0) cc_final: 0.8702 (t0) REVERT: I 95 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: I 114 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7459 (mtm110) REVERT: I 117 LEU cc_start: 0.9116 (tt) cc_final: 0.8912 (tm) REVERT: J 51 TYR cc_start: 0.9014 (p90) cc_final: 0.8730 (p90) REVERT: J 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8563 (m-30) REVERT: A 56 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8255 (mmtm) REVERT: B 523 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 551 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (pp30) REVERT: C 34 MET cc_start: 0.9450 (mmm) cc_final: 0.9196 (tpt) REVERT: C 43 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7934 (mm110) REVERT: C 54 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7260 (ttm170) REVERT: C 80 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6750 (p90) REVERT: C 213 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 25 SER cc_start: 0.8760 (m) cc_final: 0.8334 (p) REVERT: D 43 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8261 (mmmm) REVERT: D 46 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 80 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8681 (mtpm) REVERT: D 87 ASN cc_start: 0.8918 (t0) cc_final: 0.8650 (t0) REVERT: E 85 GLU cc_start: 0.8236 (tt0) cc_final: 0.7944 (tt0) REVERT: E 87 ASP cc_start: 0.8748 (m-30) cc_final: 0.8356 (m-30) REVERT: E 94 ASP cc_start: 0.8182 (t0) cc_final: 0.7918 (t70) REVERT: E 108 LYS cc_start: 0.8815 (tptm) cc_final: 0.8491 (tptp) REVERT: K 54 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7634 (tpt90) REVERT: K 56 LYS cc_start: 0.8657 (mptt) cc_final: 0.8372 (mmtt) REVERT: K 120 GLU cc_start: 0.8418 (pm20) cc_final: 0.8163 (pm20) REVERT: L 523 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 545 GLU cc_start: 0.8532 (mp0) cc_final: 0.8256 (mp0) REVERT: M 59 ASP cc_start: 0.8415 (t0) cc_final: 0.8034 (t0) REVERT: M 156 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8328 (ttp80) REVERT: N 6 GLU cc_start: 0.8060 (mp0) cc_final: 0.7838 (mp0) REVERT: N 28 THR cc_start: 0.8735 (m) cc_final: 0.8406 (t) REVERT: N 43 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8408 (mmmm) REVERT: N 46 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7543 (tm-30) REVERT: N 87 ASN cc_start: 0.8825 (t0) cc_final: 0.8619 (t0) REVERT: N 95 MET cc_start: 0.8537 (mtp) cc_final: 0.7735 (ttm) REVERT: O 16 GLN cc_start: 0.8249 (pt0) cc_final: 0.7977 (pp30) REVERT: O 44 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8710 (p) REVERT: O 87 ASP cc_start: 0.8808 (m-30) cc_final: 0.8518 (m-30) REVERT: O 108 LYS cc_start: 0.8811 (tptm) cc_final: 0.8427 (tptp) outliers start: 60 outliers final: 24 residues processed: 340 average time/residue: 1.4446 time to fit residues: 542.2500 Evaluate side-chains 308 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 2.9990 chunk 171 optimal weight: 0.0470 chunk 66 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.8096 ------------------------------------------------------------------------------- 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 N 86 ASN N 103 GLN ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058807 restraints weight = 45648.874| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.22 r_work: 0.2960 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17391 Z= 0.230 Angle : 0.604 10.919 23613 Z= 0.305 Chirality : 0.042 0.157 2634 Planarity : 0.004 0.049 3000 Dihedral : 7.504 61.020 2781 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.53 % Allowed : 18.60 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2127 helix: 1.00 (0.42), residues: 156 sheet: 0.09 (0.19), residues: 741 loop : -0.15 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE N 70 TYR 0.027 0.001 TYR E 51 ARG 0.009 0.001 ARG N 114 *********************** 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 359 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 296 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8561 (mt0) cc_final: 0.7992 (mm-40) REVERT: F 56 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8183 (mmtm) REVERT: F 100 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: F 127 ASP cc_start: 0.8351 (p0) cc_final: 0.7919 (p0) REVERT: G 523 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7342 (tm-30) REVERT: H 90 ASP cc_start: 0.6675 (m-30) cc_final: 0.6450 (m-30) REVERT: I 6 GLU cc_start: 0.8072 (mp0) cc_final: 0.7630 (mp0) REVERT: I 43 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8205 (tttm) REVERT: I 46 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: I 85 MET cc_start: 0.8450 (mtt) cc_final: 0.8177 (mtt) REVERT: I 87 ASN cc_start: 0.8919 (t0) cc_final: 0.8657 (t0) REVERT: I 95 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7813 (ttm) REVERT: I 114 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7530 (mtm110) REVERT: I 117 LEU cc_start: 0.9144 (tt) cc_final: 0.8922 (tm) REVERT: J 16 GLN cc_start: 0.7904 (pt0) cc_final: 0.7541 (pt0) REVERT: J 51 TYR cc_start: 0.8965 (p90) cc_final: 0.8733 (p90) REVERT: J 87 ASP cc_start: 0.8878 (m-30) cc_final: 0.8555 (m-30) REVERT: J 94 ASP cc_start: 0.8070 (t0) cc_final: 0.7795 (t70) REVERT: J 96 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8424 (mtm-85) REVERT: J 98 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8110 (mpp80) REVERT: A 56 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8244 (mmtm) REVERT: B 523 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 551 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7462 (pp30) REVERT: C 13 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8702 (mmmm) REVERT: C 54 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7251 (ttm170) REVERT: C 213 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8601 (mm) REVERT: D 25 SER cc_start: 0.8796 (m) cc_final: 0.8316 (p) REVERT: D 46 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: D 87 ASN cc_start: 0.8949 (t0) cc_final: 0.8699 (t0) REVERT: D 95 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7449 (ttm) REVERT: D 114 ARG cc_start: 0.7221 (mpt180) cc_final: 0.6918 (mpt180) REVERT: E 81 GLN cc_start: 0.8865 (mp10) cc_final: 0.8453 (mp10) REVERT: E 85 GLU cc_start: 0.8298 (tt0) cc_final: 0.7982 (tt0) REVERT: E 87 ASP cc_start: 0.8757 (m-30) cc_final: 0.8390 (m-30) REVERT: E 94 ASP cc_start: 0.8069 (t0) cc_final: 0.7816 (t70) REVERT: E 108 LYS cc_start: 0.8827 (tptm) cc_final: 0.8466 (tptp) REVERT: K 77 THR cc_start: 0.8838 (p) cc_final: 0.8585 (t) REVERT: L 523 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7246 (tm-30) REVERT: L 545 GLU cc_start: 0.8527 (mp0) cc_final: 0.8297 (mp0) REVERT: L 551 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7615 (pp30) REVERT: M 41 PRO cc_start: 0.8622 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8376 (t0) cc_final: 0.8016 (t0) REVERT: M 213 ILE cc_start: 0.8710 (mp) cc_final: 0.8418 (mm) REVERT: N 6 GLU cc_start: 0.8009 (mp0) cc_final: 0.7659 (mp0) REVERT: N 46 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7539 (tm-30) REVERT: N 87 ASN cc_start: 0.8894 (t0) cc_final: 0.8629 (t0) REVERT: N 95 MET cc_start: 0.8601 (mtp) cc_final: 0.7805 (ttm) REVERT: O 16 GLN cc_start: 0.8266 (pt0) cc_final: 0.8022 (pp30) REVERT: O 81 GLN cc_start: 0.8937 (mp10) cc_final: 0.8625 (mp10) REVERT: O 87 ASP cc_start: 0.8929 (m-30) cc_final: 0.8610 (m-30) REVERT: O 94 ASP cc_start: 0.8099 (t70) cc_final: 0.7504 (t70) REVERT: O 108 LYS cc_start: 0.8778 (tptm) cc_final: 0.8440 (tptp) outliers start: 63 outliers final: 33 residues processed: 325 average time/residue: 1.5196 time to fit residues: 542.5100 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 : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain L residue 551 GLN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 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: 4.9990 chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057504 restraints weight = 46329.683| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.23 r_work: 0.2925 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17391 Z= 0.329 Angle : 0.629 9.440 23613 Z= 0.320 Chirality : 0.043 0.159 2634 Planarity : 0.004 0.058 3000 Dihedral : 7.425 59.731 2781 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.59 % Allowed : 18.60 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2127 helix: 1.15 (0.42), residues: 156 sheet: -0.01 (0.19), residues: 735 loop : -0.22 (0.18), residues: 1236 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 0.028 0.001 TYR E 51 ARG 0.010 0.001 ARG N 114 *********************** 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 358 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 294 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8633 (mt0) cc_final: 0.8051 (mm-40) REVERT: F 56 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8202 (mmtm) REVERT: F 127 ASP cc_start: 0.8417 (p0) cc_final: 0.7986 (p0) REVERT: G 523 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7087 (tm-30) REVERT: H 146 HIS cc_start: 0.7424 (m90) cc_final: 0.7177 (m90) REVERT: I 6 GLU cc_start: 0.8079 (mp0) cc_final: 0.7587 (mp0) REVERT: I 46 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: I 85 MET cc_start: 0.8480 (mtt) cc_final: 0.8239 (mtt) REVERT: I 87 ASN cc_start: 0.8944 (t0) cc_final: 0.8681 (t0) REVERT: I 95 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7780 (ttm) REVERT: I 114 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7521 (mtm110) REVERT: I 117 LEU cc_start: 0.9129 (tt) cc_final: 0.8895 (tm) REVERT: J 16 GLN cc_start: 0.8039 (pt0) cc_final: 0.7708 (pt0) REVERT: J 26 TYR cc_start: 0.9425 (p90) cc_final: 0.9137 (p90) REVERT: J 41 LEU cc_start: 0.8697 (mt) cc_final: 0.8417 (mm) REVERT: J 51 TYR cc_start: 0.9010 (p90) cc_final: 0.8785 (p90) REVERT: J 68 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8457 (tmmm) REVERT: J 87 ASP cc_start: 0.8897 (m-30) cc_final: 0.8568 (m-30) REVERT: J 96 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8389 (mtm-85) REVERT: J 98 ARG cc_start: 0.8631 (mtt90) cc_final: 0.8194 (mpp80) REVERT: A 56 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8269 (mmtm) REVERT: B 523 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7122 (tm-30) REVERT: B 551 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7429 (pp30) REVERT: C 13 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8720 (mmmm) REVERT: C 34 MET cc_start: 0.9398 (mmm) cc_final: 0.9150 (tpt) REVERT: C 41 PRO cc_start: 0.8681 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8672 (mt-10) REVERT: C 54 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7238 (ttm110) REVERT: C 213 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8631 (mm) REVERT: D 25 SER cc_start: 0.8831 (m) cc_final: 0.8307 (p) REVERT: D 46 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: D 87 ASN cc_start: 0.9004 (t0) cc_final: 0.8772 (t0) REVERT: E 81 GLN cc_start: 0.8799 (mp10) cc_final: 0.8420 (mp10) REVERT: E 85 GLU cc_start: 0.8353 (tt0) cc_final: 0.8081 (tt0) REVERT: E 87 ASP cc_start: 0.8787 (m-30) cc_final: 0.8413 (m-30) REVERT: E 108 LYS cc_start: 0.8863 (tptm) cc_final: 0.8519 (tptp) REVERT: L 523 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7343 (tm-30) REVERT: L 545 GLU cc_start: 0.8565 (mp0) cc_final: 0.8245 (mp0) REVERT: M 11 LEU cc_start: 0.8875 (tp) cc_final: 0.8659 (tp) REVERT: M 41 PRO cc_start: 0.8687 (Cg_exo) cc_final: 0.8452 (Cg_endo) REVERT: M 59 ASP cc_start: 0.8297 (t0) cc_final: 0.7987 (t0) REVERT: M 156 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8131 (ttp80) REVERT: N 6 GLU cc_start: 0.8030 (mp0) cc_final: 0.7574 (mp0) REVERT: N 46 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7538 (tm-30) REVERT: N 85 MET cc_start: 0.8535 (mtt) cc_final: 0.8057 (mtt) REVERT: N 87 ASN cc_start: 0.8980 (t0) cc_final: 0.8735 (t0) REVERT: N 95 MET cc_start: 0.8667 (mtp) cc_final: 0.7803 (ttm) REVERT: N 114 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7683 (mtm110) REVERT: O 16 GLN cc_start: 0.8192 (pt0) cc_final: 0.7937 (pp30) REVERT: O 81 GLN cc_start: 0.8915 (mp10) cc_final: 0.8597 (mp10) REVERT: O 108 LYS cc_start: 0.8827 (tptm) cc_final: 0.8470 (tptp) outliers start: 64 outliers final: 31 residues processed: 323 average time/residue: 1.5205 time to fit residues: 540.0456 Evaluate side-chains 318 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain 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 232 THR Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 100 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059140 restraints weight = 45874.659| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.25 r_work: 0.2960 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17391 Z= 0.197 Angle : 0.619 9.599 23613 Z= 0.311 Chirality : 0.042 0.154 2634 Planarity : 0.004 0.046 3000 Dihedral : 7.032 59.895 2781 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.14 % Allowed : 19.50 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.18), residues: 2127 helix: 1.28 (0.42), residues: 156 sheet: 0.05 (0.19), residues: 729 loop : -0.25 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.000 HIS H 35 PHE 0.007 0.001 PHE M 211 TYR 0.028 0.001 TYR E 51 ARG 0.009 0.001 ARG A 219 *********************** 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 355 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8601 (mt0) cc_final: 0.8096 (mm-40) REVERT: F 54 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8032 (ptm-80) REVERT: F 56 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8160 (mmtm) REVERT: F 127 ASP cc_start: 0.8373 (p0) cc_final: 0.7900 (p0) REVERT: G 523 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7265 (tm-30) REVERT: H 90 ASP cc_start: 0.6763 (m-30) cc_final: 0.6534 (m-30) REVERT: H 156 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8340 (ttp80) REVERT: I 46 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: I 87 ASN cc_start: 0.8957 (t0) cc_final: 0.8697 (t0) REVERT: I 95 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7843 (ttm) REVERT: I 117 LEU cc_start: 0.9104 (tt) cc_final: 0.8860 (tm) REVERT: J 16 GLN cc_start: 0.7830 (pt0) cc_final: 0.7448 (pp30) REVERT: J 26 TYR cc_start: 0.9424 (p90) cc_final: 0.9132 (p90) REVERT: J 68 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8300 (tmmm) REVERT: J 87 ASP cc_start: 0.8881 (m-30) cc_final: 0.8545 (m-30) REVERT: J 94 ASP cc_start: 0.8049 (t0) cc_final: 0.7780 (t70) REVERT: J 96 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8378 (mtm-85) REVERT: J 98 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8075 (mpp80) REVERT: B 523 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7263 (tm-30) REVERT: B 551 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: C 13 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8720 (mmmm) REVERT: C 34 MET cc_start: 0.9447 (mmm) cc_final: 0.9215 (tpt) REVERT: C 40 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7672 (tpp80) REVERT: C 41 PRO cc_start: 0.8653 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: C 43 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8022 (mm110) REVERT: C 46 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8665 (mt-10) REVERT: C 89 GLU cc_start: 0.8221 (pp20) cc_final: 0.7868 (pp20) REVERT: C 213 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8549 (mm) REVERT: D 25 SER cc_start: 0.8792 (m) cc_final: 0.8302 (p) REVERT: D 46 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: D 67 ARG cc_start: 0.7775 (pmt-80) cc_final: 0.6744 (tpp80) REVERT: D 87 ASN cc_start: 0.9020 (t0) cc_final: 0.8785 (t0) REVERT: D 95 MET cc_start: 0.8190 (mtp) cc_final: 0.7668 (ttm) REVERT: E 81 GLN cc_start: 0.8812 (mp10) cc_final: 0.8446 (mp10) REVERT: E 85 GLU cc_start: 0.8344 (tt0) cc_final: 0.8078 (tt0) REVERT: E 87 ASP cc_start: 0.8787 (m-30) cc_final: 0.8395 (m-30) REVERT: E 94 ASP cc_start: 0.7976 (t0) cc_final: 0.7746 (t70) REVERT: E 108 LYS cc_start: 0.8875 (tptm) cc_final: 0.8535 (tptp) REVERT: E 109 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8259 (tp) REVERT: L 523 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7298 (tm-30) REVERT: L 545 GLU cc_start: 0.8498 (mp0) cc_final: 0.8196 (mp0) REVERT: M 11 LEU cc_start: 0.8890 (tp) cc_final: 0.8648 (tp) REVERT: M 59 ASP cc_start: 0.8212 (t0) cc_final: 0.7909 (t0) REVERT: M 89 GLU cc_start: 0.8038 (pp20) cc_final: 0.7689 (pp20) REVERT: M 156 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8282 (ttp80) REVERT: M 213 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8499 (mm) REVERT: N 6 GLU cc_start: 0.7897 (mp0) cc_final: 0.7681 (mp0) REVERT: N 46 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7610 (tm-30) REVERT: N 85 MET cc_start: 0.8382 (mtt) cc_final: 0.7861 (mtt) REVERT: N 87 ASN cc_start: 0.9015 (t0) cc_final: 0.8787 (t0) REVERT: N 95 MET cc_start: 0.8648 (mtp) cc_final: 0.7789 (ttm) REVERT: N 114 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7831 (mtm110) REVERT: O 16 GLN cc_start: 0.8147 (pt0) cc_final: 0.7906 (pp30) REVERT: O 41 LEU cc_start: 0.8840 (mm) cc_final: 0.8511 (mm) REVERT: O 47 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8846 (ttmm) REVERT: O 81 GLN cc_start: 0.8906 (mp10) cc_final: 0.8558 (mp10) REVERT: O 94 ASP cc_start: 0.8110 (t70) cc_final: 0.7598 (t70) REVERT: O 108 LYS cc_start: 0.8799 (tptm) cc_final: 0.8456 (tptt) outliers start: 56 outliers final: 28 residues processed: 328 average time/residue: 1.4835 time to fit residues: 536.3160 Evaluate side-chains 316 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 52 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 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 52 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 47 LYS 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: 0.0000 chunk 206 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058585 restraints weight = 45641.455| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.23 r_work: 0.2956 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17391 Z= 0.243 Angle : 0.638 8.495 23613 Z= 0.320 Chirality : 0.043 0.170 2634 Planarity : 0.004 0.084 3000 Dihedral : 6.914 58.616 2781 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.91 % Allowed : 21.01 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2127 helix: 1.36 (0.43), residues: 156 sheet: -0.10 (0.19), residues: 756 loop : -0.20 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE I 70 TYR 0.028 0.001 TYR E 51 ARG 0.014 0.001 ARG I 114 *********************** 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 351 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8614 (mt0) cc_final: 0.8107 (mm-40) REVERT: F 54 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8049 (ptm-80) REVERT: F 56 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8181 (mmtm) REVERT: F 127 ASP cc_start: 0.8401 (p0) cc_final: 0.7947 (p0) REVERT: G 523 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7208 (tm-30) REVERT: H 146 HIS cc_start: 0.7401 (m90) cc_final: 0.7149 (m90) REVERT: I 46 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: I 87 ASN cc_start: 0.8959 (t0) cc_final: 0.8730 (t0) REVERT: I 95 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7831 (ttm) REVERT: I 117 LEU cc_start: 0.9082 (tt) cc_final: 0.8833 (tm) REVERT: J 16 GLN cc_start: 0.7831 (pt0) cc_final: 0.7486 (pt0) REVERT: J 26 TYR cc_start: 0.9432 (p90) cc_final: 0.9212 (p90) REVERT: J 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8561 (m-30) REVERT: J 94 ASP cc_start: 0.8103 (t0) cc_final: 0.7807 (t70) REVERT: J 96 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8432 (mtm-85) REVERT: J 98 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8113 (mpp80) REVERT: B 523 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 551 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7408 (pp30) REVERT: C 13 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8724 (mmmm) REVERT: C 34 MET cc_start: 0.9428 (mmm) cc_final: 0.9204 (tpt) REVERT: C 46 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 54 ARG cc_start: 0.7637 (ttp-170) cc_final: 0.7147 (ttm170) REVERT: C 59 ASP cc_start: 0.8342 (t0) cc_final: 0.8095 (t0) REVERT: C 89 GLU cc_start: 0.8218 (pp20) cc_final: 0.7921 (pp20) REVERT: C 213 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 25 SER cc_start: 0.8767 (m) cc_final: 0.8236 (p) REVERT: D 39 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 46 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: D 95 MET cc_start: 0.8230 (mtp) cc_final: 0.7650 (ttm) REVERT: E 68 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8163 (tmmm) REVERT: E 81 GLN cc_start: 0.8816 (mp10) cc_final: 0.8436 (mp10) REVERT: E 85 GLU cc_start: 0.8374 (tt0) cc_final: 0.8170 (tt0) REVERT: E 87 ASP cc_start: 0.8801 (m-30) cc_final: 0.8377 (m-30) REVERT: E 94 ASP cc_start: 0.8153 (t0) cc_final: 0.7921 (t70) REVERT: E 98 ARG cc_start: 0.8424 (mpp80) cc_final: 0.8166 (mpp80) REVERT: E 108 LYS cc_start: 0.8898 (tptm) cc_final: 0.8569 (tptp) REVERT: L 522 ASP cc_start: 0.7530 (t70) cc_final: 0.7152 (t0) REVERT: L 523 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7415 (tm-30) REVERT: L 545 GLU cc_start: 0.8487 (mp0) cc_final: 0.8174 (mp0) REVERT: M 11 LEU cc_start: 0.8885 (tp) cc_final: 0.8638 (tp) REVERT: M 59 ASP cc_start: 0.8211 (t0) cc_final: 0.7903 (t0) REVERT: M 156 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8275 (ttp80) REVERT: M 213 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8573 (mm) REVERT: N 6 GLU cc_start: 0.7912 (mp0) cc_final: 0.7605 (mp0) REVERT: N 39 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8460 (tm-30) REVERT: N 46 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7615 (tm-30) REVERT: N 85 MET cc_start: 0.8370 (mtt) cc_final: 0.7881 (mtt) REVERT: N 87 ASN cc_start: 0.8947 (t0) cc_final: 0.8732 (t0) REVERT: N 95 MET cc_start: 0.8671 (mtp) cc_final: 0.7767 (ttm) REVERT: N 114 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7833 (mtm110) REVERT: O 16 GLN cc_start: 0.8140 (pt0) cc_final: 0.7900 (pp30) REVERT: O 81 GLN cc_start: 0.8885 (mp10) cc_final: 0.8577 (mp10) REVERT: O 94 ASP cc_start: 0.8128 (t70) cc_final: 0.7640 (t70) REVERT: O 108 LYS cc_start: 0.8831 (tptm) cc_final: 0.8481 (tptt) outliers start: 52 outliers final: 33 residues processed: 324 average time/residue: 1.5070 time to fit residues: 537.4077 Evaluate side-chains 328 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058655 restraints weight = 45493.211| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.22 r_work: 0.2957 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17391 Z= 0.250 Angle : 0.648 8.803 23613 Z= 0.326 Chirality : 0.043 0.178 2634 Planarity : 0.004 0.047 3000 Dihedral : 6.829 58.102 2781 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.75 % Allowed : 21.90 % Favored : 75.35 % 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: 1.37 (0.43), residues: 156 sheet: -0.07 (0.19), residues: 738 loop : -0.23 (0.18), residues: 1233 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 0.010 0.001 PHE I 70 TYR 0.030 0.001 TYR J 51 ARG 0.014 0.001 ARG I 114 *********************** 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 344 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8611 (mt0) cc_final: 0.8106 (mm-40) REVERT: F 54 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8046 (ptm-80) REVERT: F 56 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8186 (mmtm) REVERT: F 127 ASP cc_start: 0.8376 (p0) cc_final: 0.7942 (p0) REVERT: G 523 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7194 (tm-30) REVERT: G 540 GLU cc_start: 0.8647 (pm20) cc_final: 0.8401 (mp0) REVERT: H 146 HIS cc_start: 0.7447 (m90) cc_final: 0.7191 (m90) REVERT: I 46 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: I 95 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7815 (ttm) REVERT: I 117 LEU cc_start: 0.9082 (tt) cc_final: 0.8825 (tm) REVERT: J 16 GLN cc_start: 0.7913 (pt0) cc_final: 0.7574 (pt0) REVERT: J 26 TYR cc_start: 0.9424 (p90) cc_final: 0.9127 (p90) REVERT: J 87 ASP cc_start: 0.8902 (m-30) cc_final: 0.8562 (m-30) REVERT: J 94 ASP cc_start: 0.8107 (t0) cc_final: 0.7803 (t70) REVERT: J 96 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8411 (mtm-85) REVERT: J 98 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8121 (mpp80) REVERT: B 523 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 551 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7422 (pp30) REVERT: C 13 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8727 (mmmm) REVERT: C 34 MET cc_start: 0.9431 (mmm) cc_final: 0.9204 (tpt) REVERT: C 40 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7815 (tpp80) REVERT: C 46 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8678 (mt-10) REVERT: C 54 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7226 (ttm110) REVERT: C 59 ASP cc_start: 0.8369 (t0) cc_final: 0.8095 (t0) REVERT: C 213 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 25 SER cc_start: 0.8760 (m) cc_final: 0.8227 (p) REVERT: D 39 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 46 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 95 MET cc_start: 0.8249 (mtp) cc_final: 0.7649 (ttm) REVERT: E 68 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8159 (tmmm) REVERT: E 85 GLU cc_start: 0.8351 (tt0) cc_final: 0.8148 (tt0) REVERT: E 87 ASP cc_start: 0.8794 (m-30) cc_final: 0.8368 (m-30) REVERT: E 94 ASP cc_start: 0.8174 (t0) cc_final: 0.7933 (t70) REVERT: E 108 LYS cc_start: 0.8906 (tptm) cc_final: 0.8574 (tptp) REVERT: E 109 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8443 (tp) REVERT: L 522 ASP cc_start: 0.7524 (t70) cc_final: 0.7149 (t0) REVERT: L 523 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7440 (tm-30) REVERT: L 540 GLU cc_start: 0.8637 (pm20) cc_final: 0.8418 (mp0) REVERT: L 545 GLU cc_start: 0.8517 (mp0) cc_final: 0.8172 (mp0) REVERT: M 11 LEU cc_start: 0.8897 (tp) cc_final: 0.8651 (tp) REVERT: M 59 ASP cc_start: 0.8225 (t0) cc_final: 0.7912 (t0) REVERT: M 156 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8271 (ttp80) REVERT: M 213 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8572 (mm) REVERT: N 6 GLU cc_start: 0.7893 (mp0) cc_final: 0.7652 (mp0) REVERT: N 39 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8454 (tm-30) REVERT: N 46 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7618 (tm-30) REVERT: N 85 MET cc_start: 0.8364 (mtt) cc_final: 0.7859 (mtt) REVERT: N 87 ASN cc_start: 0.8961 (t0) cc_final: 0.8760 (t0) REVERT: N 95 MET cc_start: 0.8665 (mtp) cc_final: 0.7731 (ttm) REVERT: N 114 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7830 (mtm110) REVERT: O 16 GLN cc_start: 0.8099 (pt0) cc_final: 0.7855 (pp30) REVERT: O 81 GLN cc_start: 0.8907 (mp10) cc_final: 0.8543 (mp10) REVERT: O 94 ASP cc_start: 0.8127 (t70) cc_final: 0.7641 (t70) REVERT: O 108 LYS cc_start: 0.8798 (tptm) cc_final: 0.8489 (tptt) outliers start: 49 outliers final: 30 residues processed: 322 average time/residue: 1.5068 time to fit residues: 533.7071 Evaluate side-chains 325 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 110 ASP 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 M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059123 restraints weight = 45914.569| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.24 r_work: 0.2970 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17391 Z= 0.222 Angle : 0.668 8.803 23613 Z= 0.337 Chirality : 0.043 0.160 2634 Planarity : 0.004 0.047 3000 Dihedral : 6.651 56.998 2781 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.35 % Allowed : 22.75 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2127 helix: 1.44 (0.43), residues: 156 sheet: -0.09 (0.19), residues: 750 loop : -0.21 (0.18), residues: 1221 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 0.008 0.001 PHE I 70 TYR 0.029 0.001 TYR E 51 ARG 0.015 0.001 ARG I 114 *********************** 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 334 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 GLN cc_start: 0.8577 (mt0) cc_final: 0.8033 (mm-40) REVERT: F 56 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8170 (mmtm) REVERT: F 127 ASP cc_start: 0.8401 (p0) cc_final: 0.7958 (p0) REVERT: G 523 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7264 (tm-30) REVERT: G 545 GLU cc_start: 0.7891 (pp20) cc_final: 0.7677 (tm-30) REVERT: H 80 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: H 146 HIS cc_start: 0.7402 (m90) cc_final: 0.7139 (m90) REVERT: I 39 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8281 (tm-30) REVERT: I 46 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: I 85 MET cc_start: 0.8371 (mpp) cc_final: 0.7873 (mpp) REVERT: I 95 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7804 (ttm) REVERT: I 117 LEU cc_start: 0.9085 (tt) cc_final: 0.8827 (tm) REVERT: J 16 GLN cc_start: 0.7887 (pt0) cc_final: 0.7555 (pt0) REVERT: J 26 TYR cc_start: 0.9421 (p90) cc_final: 0.9132 (p90) REVERT: J 87 ASP cc_start: 0.8863 (m-30) cc_final: 0.8533 (m-30) REVERT: J 94 ASP cc_start: 0.8074 (t0) cc_final: 0.7766 (t70) REVERT: J 96 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8384 (mtm-85) REVERT: J 98 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8080 (mpp80) REVERT: A 56 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8216 (mmtm) REVERT: A 156 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 523 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 551 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7351 (pp30) REVERT: C 13 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8731 (mmmm) REVERT: C 34 MET cc_start: 0.9441 (mmm) cc_final: 0.9211 (tpt) REVERT: C 40 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7901 (tpp80) REVERT: C 46 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8688 (mt-10) REVERT: C 59 ASP cc_start: 0.8417 (t0) cc_final: 0.8104 (t0) REVERT: C 62 GLU cc_start: 0.8486 (pt0) cc_final: 0.8115 (pm20) REVERT: C 213 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8558 (mm) REVERT: D 25 SER cc_start: 0.8777 (m) cc_final: 0.8268 (p) REVERT: D 39 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8377 (tm-30) REVERT: D 46 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: D 95 MET cc_start: 0.8158 (mtp) cc_final: 0.7544 (ttm) REVERT: D 114 ARG cc_start: 0.6975 (mpt180) cc_final: 0.6671 (mpt180) REVERT: E 68 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8121 (tmmm) REVERT: E 85 GLU cc_start: 0.8372 (tt0) cc_final: 0.8169 (tt0) REVERT: E 94 ASP cc_start: 0.8146 (t0) cc_final: 0.7901 (t70) REVERT: E 98 ARG cc_start: 0.8372 (mpp80) cc_final: 0.8093 (mpp80) REVERT: E 108 LYS cc_start: 0.8893 (tptm) cc_final: 0.8560 (tptp) REVERT: E 109 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8428 (tp) REVERT: L 523 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7350 (tm-30) REVERT: L 545 GLU cc_start: 0.8476 (mp0) cc_final: 0.8154 (mp0) REVERT: M 13 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8724 (mmmt) REVERT: M 43 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8250 (mm110) REVERT: M 59 ASP cc_start: 0.8189 (t0) cc_final: 0.7935 (t0) REVERT: M 80 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: M 156 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8275 (ttp80) REVERT: N 6 GLU cc_start: 0.7831 (mp0) cc_final: 0.7549 (mp0) REVERT: N 39 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8434 (tm-30) REVERT: N 46 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7491 (tm-30) REVERT: N 95 MET cc_start: 0.8654 (mtp) cc_final: 0.7761 (ttm) REVERT: N 114 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7828 (mtm110) REVERT: O 16 GLN cc_start: 0.8059 (pt0) cc_final: 0.7815 (pp30) REVERT: O 81 GLN cc_start: 0.8871 (mp10) cc_final: 0.8467 (mp10) REVERT: O 108 LYS cc_start: 0.8806 (tptm) cc_final: 0.8484 (tptt) outliers start: 42 outliers final: 26 residues processed: 313 average time/residue: 1.4808 time to fit residues: 510.5123 Evaluate side-chains 313 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain 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 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 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 213 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.7207 > 50: distance: 98 - 102: 10.923 distance: 102 - 103: 18.804 distance: 103 - 104: 18.094 distance: 103 - 106: 17.550 distance: 104 - 105: 27.170 distance: 104 - 109: 45.196 distance: 106 - 107: 19.178 distance: 106 - 108: 20.497 distance: 109 - 110: 19.491 distance: 110 - 111: 26.388 distance: 111 - 112: 20.062 distance: 111 - 116: 57.639 distance: 113 - 114: 14.099 distance: 113 - 115: 20.886 distance: 116 - 117: 10.381 distance: 117 - 118: 35.288 distance: 117 - 120: 12.801 distance: 118 - 119: 20.048 distance: 118 - 124: 16.921 distance: 120 - 121: 32.062 distance: 120 - 122: 33.268 distance: 121 - 123: 26.771 distance: 124 - 125: 10.683 distance: 125 - 126: 5.713 distance: 125 - 128: 15.516 distance: 126 - 127: 14.195 distance: 126 - 135: 7.853 distance: 128 - 129: 3.607 distance: 129 - 130: 8.347 distance: 130 - 131: 13.023 distance: 131 - 132: 6.201 distance: 132 - 133: 7.200 distance: 132 - 134: 6.250 distance: 136 - 137: 6.691 distance: 136 - 139: 5.017 distance: 137 - 138: 14.074 distance: 137 - 147: 11.785 distance: 139 - 140: 14.857 distance: 140 - 141: 9.651 distance: 140 - 142: 16.763 distance: 141 - 143: 15.517 distance: 142 - 144: 20.153 distance: 143 - 145: 12.837 distance: 144 - 145: 14.859 distance: 145 - 146: 8.652 distance: 147 - 148: 4.334 distance: 148 - 149: 13.593 distance: 148 - 151: 10.756 distance: 149 - 150: 7.249 distance: 149 - 156: 13.297 distance: 151 - 152: 8.535 distance: 153 - 154: 4.786 distance: 153 - 155: 18.444 distance: 156 - 157: 10.009 distance: 157 - 158: 11.483 distance: 157 - 160: 16.041 distance: 158 - 159: 6.699 distance: 158 - 161: 10.472 distance: 161 - 162: 19.628 distance: 161 - 206: 20.891 distance: 162 - 163: 8.022 distance: 162 - 165: 5.562 distance: 163 - 164: 15.664 distance: 163 - 168: 14.220 distance: 164 - 203: 20.337 distance: 165 - 166: 6.198 distance: 165 - 167: 6.746 distance: 168 - 169: 11.671 distance: 169 - 170: 8.997 distance: 170 - 171: 8.931 distance: 170 - 172: 10.567 distance: 172 - 173: 8.237 distance: 173 - 174: 9.334 distance: 173 - 176: 9.560 distance: 174 - 175: 15.456 distance: 174 - 183: 10.957 distance: 176 - 177: 6.506 distance: 177 - 178: 6.238 distance: 177 - 179: 8.055 distance: 178 - 180: 17.463 distance: 179 - 181: 39.865 distance: 180 - 182: 28.888 distance: 181 - 182: 33.377