Starting phenix.real_space_refine on Wed Jul 30 17:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7h_27230/07_2025/8d7h_27230.cif" } resolution = 3.4 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 46 5.16 5 C 7970 2.51 5 N 2156 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "A" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "G" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.17, per 1000 atoms: 0.73 Number of scatterers: 12540 At special positions: 0 Unit cell: (196.94, 156.52, 101.48, 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 46 16.00 O 2368 8.00 N 2156 7.00 C 7970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 184 " - pdb=" SG CYS E 195 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 168 " " NAG A 502 " - " ASN A 292 " " NAG B 1 " - " ASN C 190 " " NAG E 501 " - " ASN E 168 " " NAG E 502 " - " ASN E 292 " " NAG F 1 " - " ASN C 70 " " NAG I 1 " - " ASN C 60 " " NAG J 1 " - " ASN C 142 " " NAG K 1 " - " ASN A 92 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 140 " " NAG N 1 " - " ASN G 190 " " NAG O 1 " - " ASN G 70 " " NAG P 1 " - " ASN G 60 " " NAG Q 1 " - " ASN G 142 " " NAG R 1 " - " ASN E 92 " " NAG S 1 " - " ASN E 104 " " NAG T 1 " - " ASN E 140 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 19.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N HIS C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'D' and resid 35 through 66 removed outlier: 4.252A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.625A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 208 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.819A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.526A pdb=" N HIS G 83 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER G 84 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 80 through 84' Processing helix chain 'H' and resid 35 through 66 removed outlier: 4.251A pdb=" N SER H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 90 through 97 removed outlier: 3.637A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 126 through 154 Processing helix chain 'H' and resid 176 through 208 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.948A pdb=" N LEU E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.379A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 89 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 101 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.602A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.758A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 145 removed outlier: 3.684A pdb=" N THR C 144 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 190 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 214 removed outlier: 3.657A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.544A pdb=" N GLN C 255 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 246 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 243 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.589A pdb=" N VAL A 42 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 61 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 91 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY A 132 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 125 " --> pdb=" O CYS A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 4.008A pdb=" N GLU A 186 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 156 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN A 140 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR A 234 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 145 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AB4, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.540A pdb=" N PHE A 308 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 36 removed outlier: 6.402A pdb=" N HIS G 32 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS G 104 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN G 34 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU G 97 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS G 91 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 99 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 45 removed outlier: 3.508A pdb=" N VAL G 42 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 113 through 114 removed outlier: 3.756A pdb=" N HIS G 130 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.685A pdb=" N THR G 144 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 190 " --> pdb=" O VAL G 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 211 through 214 removed outlier: 3.731A pdb=" N VAL G 224 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 255 through 258 removed outlier: 3.689A pdb=" N GLN G 255 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR G 246 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 257 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 243 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.572A pdb=" N VAL E 42 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 61 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 91 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY E 132 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 125 " --> pdb=" O CYS E 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.002A pdb=" N GLU E 186 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR E 156 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN E 140 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR E 234 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER E 145 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.538A pdb=" N PHE E 308 " --> pdb=" O ARG E 277 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4000 1.35 - 1.47: 3228 1.47 - 1.59: 5630 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 12916 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17046 1.38 - 2.76: 532 2.76 - 4.15: 68 4.15 - 5.53: 14 5.53 - 6.91: 4 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C GLY H 164 " pdb=" N THR H 165 " pdb=" CA THR H 165 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C GLY D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 angle pdb=" C HIS C 25 " pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 120.51 123.74 -3.23 1.45e+00 4.76e-01 4.95e+00 angle pdb=" C LEU C 251 " pdb=" N ASP C 252 " pdb=" CA ASP C 252 " ideal model delta sigma weight residual 122.46 125.52 -3.06 1.41e+00 5.03e-01 4.70e+00 angle pdb=" C LEU G 251 " pdb=" N ASP G 252 " pdb=" CA ASP G 252 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.81e+00 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7488 17.59 - 35.18: 438 35.18 - 52.76: 116 52.76 - 70.35: 23 70.35 - 87.94: 15 Dihedral angle restraints: 8080 sinusoidal: 3642 harmonic: 4438 Sorted by residual: dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 43.91 49.09 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 45.65 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 54.73 38.27 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1627 0.046 - 0.091: 254 0.091 - 0.137: 139 0.137 - 0.182: 0 0.182 - 0.228: 2 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN E 104 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 104 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL E 290 " pdb=" N VAL E 290 " pdb=" C VAL E 290 " pdb=" CB VAL E 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2019 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 67 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 66 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO H 67 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 66 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO E 67 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.020 5.00e-02 4.00e+02 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3481 2.81 - 3.33: 10249 3.33 - 3.86: 19416 3.86 - 4.38: 20534 4.38 - 4.90: 37340 Nonbonded interactions: 91020 Sorted by model distance: nonbonded pdb=" OD1 ASP A 120 " pdb=" OG SER A 122 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP G 197 " pdb=" OG1 THR G 200 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG C 245 " pdb=" OE1 GLN C 279 " model vdw 2.359 3.120 nonbonded pdb=" NH2 ARG G 245 " pdb=" OE1 GLN G 279 " model vdw 2.360 3.120 ... (remaining 91015 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.460 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.003 0.044 12960 Z= 0.156 Angle : 0.531 6.910 17784 Z= 0.266 Chirality : 0.041 0.228 2022 Planarity : 0.004 0.047 2228 Dihedral : 12.375 87.938 5184 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -1.37 (0.21), residues: 1514 helix: 2.16 (0.30), residues: 250 sheet: -0.29 (0.25), residues: 456 loop : -2.42 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 254 HIS 0.004 0.000 HIS G 83 PHE 0.004 0.000 PHE H 74 TYR 0.005 0.000 TYR C 136 ARG 0.001 0.000 ARG G 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 18) link_NAG-ASN : angle 0.89087 ( 54) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 0.89759 ( 42) hydrogen bonds : bond 0.21798 ( 419) hydrogen bonds : angle 7.12612 ( 1167) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.85675 ( 24) covalent geometry : bond 0.00320 (12916) covalent geometry : angle 0.52760 (17664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 HIS cc_start: 0.4518 (m-70) cc_final: 0.4266 (m-70) REVERT: C 104 HIS cc_start: 0.7099 (m-70) cc_final: 0.6777 (m-70) REVERT: C 226 TRP cc_start: 0.8827 (p90) cc_final: 0.8561 (p90) REVERT: D 117 LEU cc_start: 0.7648 (tt) cc_final: 0.7446 (tt) REVERT: D 209 MET cc_start: 0.5983 (tpp) cc_final: 0.5263 (mtt) REVERT: A 57 LEU cc_start: 0.7672 (tp) cc_final: 0.7432 (mp) REVERT: G 83 HIS cc_start: 0.4061 (m170) cc_final: 0.3807 (m-70) REVERT: G 226 TRP cc_start: 0.8708 (p90) cc_final: 0.8409 (p90) REVERT: H 209 MET cc_start: 0.6323 (tpp) cc_final: 0.5666 (mtt) REVERT: E 57 LEU cc_start: 0.7761 (tp) cc_final: 0.7393 (mp) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.2720 time to fit residues: 81.8227 Evaluate side-chains 142 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.0000 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 83 HIS C 265 HIS C 285 ASN D 105 GLN A 113 ASN A 196 HIS G 265 HIS G 285 ASN H 105 GLN H 175 HIS E 113 ASN E 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.194861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146035 restraints weight = 18103.247| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.24 r_work: 0.3600 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.127 Angle : 0.612 11.541 17784 Z= 0.287 Chirality : 0.045 0.378 2022 Planarity : 0.004 0.048 2228 Dihedral : 5.355 55.424 2342 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.87 % Allowed : 12.67 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.49 (0.22), residues: 1514 helix: 3.00 (0.32), residues: 252 sheet: 0.28 (0.25), residues: 460 loop : -1.92 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 57 HIS 0.004 0.001 HIS C 265 PHE 0.009 0.001 PHE H 185 TYR 0.014 0.001 TYR H 49 ARG 0.006 0.000 ARG A 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 18) link_NAG-ASN : angle 3.50689 ( 54) link_BETA1-4 : bond 0.00432 ( 14) link_BETA1-4 : angle 1.86672 ( 42) hydrogen bonds : bond 0.04663 ( 419) hydrogen bonds : angle 4.96511 ( 1167) SS BOND : bond 0.00384 ( 12) SS BOND : angle 1.44869 ( 24) covalent geometry : bond 0.00286 (12916) covalent geometry : angle 0.57327 (17664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7292 (m-70) cc_final: 0.6938 (m-70) REVERT: C 117 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7836 (ptt-90) REVERT: C 226 TRP cc_start: 0.8835 (p90) cc_final: 0.8372 (p90) REVERT: D 201 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7104 (m-30) REVERT: D 209 MET cc_start: 0.6045 (tpp) cc_final: 0.5291 (mtt) REVERT: A 57 LEU cc_start: 0.8051 (tp) cc_final: 0.7715 (mp) REVERT: A 340 ARG cc_start: 0.8125 (ptt90) cc_final: 0.7771 (ptt-90) REVERT: G 104 HIS cc_start: 0.7101 (m-70) cc_final: 0.6676 (m-70) REVERT: G 226 TRP cc_start: 0.8677 (p90) cc_final: 0.8196 (p90) REVERT: H 201 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: H 209 MET cc_start: 0.6370 (tpp) cc_final: 0.5889 (mtt) REVERT: E 57 LEU cc_start: 0.8131 (tp) cc_final: 0.7685 (mp) outliers start: 38 outliers final: 16 residues processed: 171 average time/residue: 0.1907 time to fit residues: 51.1285 Evaluate side-chains 142 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 145 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS G 83 HIS G 100 GLN H 70 ASN E 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.193164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143741 restraints weight = 18116.818| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 4.06 r_work: 0.3594 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12960 Z= 0.107 Angle : 0.576 12.717 17784 Z= 0.269 Chirality : 0.044 0.342 2022 Planarity : 0.004 0.050 2228 Dihedral : 5.090 54.053 2340 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.04 % Allowed : 13.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.05 (0.22), residues: 1514 helix: 3.41 (0.32), residues: 252 sheet: 0.59 (0.25), residues: 456 loop : -1.66 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.003 0.000 HIS G 83 PHE 0.023 0.001 PHE E 266 TYR 0.014 0.001 TYR H 49 ARG 0.004 0.000 ARG A 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 18) link_NAG-ASN : angle 3.20684 ( 54) link_BETA1-4 : bond 0.00330 ( 14) link_BETA1-4 : angle 1.38013 ( 42) hydrogen bonds : bond 0.04004 ( 419) hydrogen bonds : angle 4.60441 ( 1167) SS BOND : bond 0.00279 ( 12) SS BOND : angle 1.19295 ( 24) covalent geometry : bond 0.00241 (12916) covalent geometry : angle 0.54426 (17664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7113 (m-70) cc_final: 0.6824 (m-70) REVERT: C 117 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7653 (ptt-90) REVERT: C 226 TRP cc_start: 0.8814 (p90) cc_final: 0.8331 (p90) REVERT: D 201 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: D 209 MET cc_start: 0.5937 (tpp) cc_final: 0.5205 (mtt) REVERT: A 57 LEU cc_start: 0.8089 (tp) cc_final: 0.7759 (mp) REVERT: A 340 ARG cc_start: 0.8075 (ptt90) cc_final: 0.7735 (ptt-90) REVERT: G 246 TYR cc_start: 0.6079 (p90) cc_final: 0.5558 (p90) REVERT: H 201 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: H 209 MET cc_start: 0.6304 (tpp) cc_final: 0.5821 (mtt) REVERT: E 57 LEU cc_start: 0.8162 (tp) cc_final: 0.7722 (mp) outliers start: 27 outliers final: 17 residues processed: 142 average time/residue: 0.2039 time to fit residues: 46.3535 Evaluate side-chains 136 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 146 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS G 256 HIS H 53 GLN H 106 ASN E 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.187949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137734 restraints weight = 17694.773| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.00 r_work: 0.3506 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.127 Angle : 0.600 15.847 17784 Z= 0.280 Chirality : 0.047 0.602 2022 Planarity : 0.004 0.053 2228 Dihedral : 5.054 51.982 2340 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.64 % Allowed : 14.93 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1514 helix: 3.66 (0.32), residues: 246 sheet: 0.80 (0.25), residues: 454 loop : -1.48 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.004 0.001 HIS G 83 PHE 0.016 0.002 PHE E 266 TYR 0.012 0.001 TYR H 49 ARG 0.003 0.000 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 18) link_NAG-ASN : angle 3.78450 ( 54) link_BETA1-4 : bond 0.00349 ( 14) link_BETA1-4 : angle 1.73667 ( 42) hydrogen bonds : bond 0.04712 ( 419) hydrogen bonds : angle 4.43668 ( 1167) SS BOND : bond 0.00313 ( 12) SS BOND : angle 1.12827 ( 24) covalent geometry : bond 0.00294 (12916) covalent geometry : angle 0.55627 (17664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7264 (m-70) cc_final: 0.6986 (m-70) REVERT: C 111 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6601 (pm20) REVERT: C 117 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: D 201 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: D 209 MET cc_start: 0.6158 (tpp) cc_final: 0.5419 (mtt) REVERT: A 57 LEU cc_start: 0.8144 (tp) cc_final: 0.7819 (mp) REVERT: A 340 ARG cc_start: 0.8052 (ptt90) cc_final: 0.7718 (ptt-90) REVERT: G 246 TYR cc_start: 0.6195 (p90) cc_final: 0.5757 (p90) REVERT: H 201 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: H 209 MET cc_start: 0.6365 (tpp) cc_final: 0.5921 (mtt) REVERT: E 57 LEU cc_start: 0.8223 (tp) cc_final: 0.7785 (mp) outliers start: 35 outliers final: 22 residues processed: 145 average time/residue: 0.2010 time to fit residues: 46.9593 Evaluate side-chains 140 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 121 optimal weight: 0.1980 chunk 67 optimal weight: 0.0030 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 139 optimal weight: 0.0010 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 83 HIS G 165 HIS G 285 ASN H 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140925 restraints weight = 17301.286| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.43 r_work: 0.3559 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12960 Z= 0.100 Angle : 0.552 11.371 17784 Z= 0.261 Chirality : 0.044 0.421 2022 Planarity : 0.004 0.051 2228 Dihedral : 4.716 46.090 2340 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.32 % Allowed : 14.56 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.51 (0.23), residues: 1514 helix: 3.75 (0.32), residues: 252 sheet: 0.88 (0.25), residues: 458 loop : -1.20 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.002 0.000 HIS G 83 PHE 0.014 0.001 PHE A 266 TYR 0.011 0.001 TYR H 49 ARG 0.002 0.000 ARG A 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 18) link_NAG-ASN : angle 3.14288 ( 54) link_BETA1-4 : bond 0.00534 ( 14) link_BETA1-4 : angle 1.18033 ( 42) hydrogen bonds : bond 0.03970 ( 419) hydrogen bonds : angle 4.18261 ( 1167) SS BOND : bond 0.00301 ( 12) SS BOND : angle 0.95982 ( 24) covalent geometry : bond 0.00227 (12916) covalent geometry : angle 0.52115 (17664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7335 (m-70) cc_final: 0.7105 (m-70) REVERT: C 117 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7836 (ptt-90) REVERT: C 190 ASN cc_start: 0.6598 (OUTLIER) cc_final: 0.6367 (m-40) REVERT: C 234 ASP cc_start: 0.7435 (t0) cc_final: 0.7077 (t0) REVERT: D 201 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: D 209 MET cc_start: 0.6144 (tpp) cc_final: 0.5419 (mtt) REVERT: A 57 LEU cc_start: 0.8189 (tp) cc_final: 0.7837 (mp) REVERT: A 340 ARG cc_start: 0.7850 (ptt90) cc_final: 0.7588 (ptt-90) REVERT: G 246 TYR cc_start: 0.6181 (p90) cc_final: 0.5768 (p90) REVERT: H 201 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: H 209 MET cc_start: 0.6330 (tpp) cc_final: 0.5938 (mtt) REVERT: E 57 LEU cc_start: 0.8248 (tp) cc_final: 0.7837 (mp) outliers start: 44 outliers final: 23 residues processed: 154 average time/residue: 0.1894 time to fit residues: 46.6282 Evaluate side-chains 142 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.0010 chunk 34 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 83 HIS G 285 ASN H 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.188170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137914 restraints weight = 17987.347| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.08 r_work: 0.3511 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12960 Z= 0.110 Angle : 0.584 12.841 17784 Z= 0.274 Chirality : 0.046 0.562 2022 Planarity : 0.004 0.054 2228 Dihedral : 4.616 44.387 2340 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.94 % Allowed : 14.86 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.55 (0.22), residues: 1514 helix: 3.84 (0.31), residues: 246 sheet: 0.89 (0.25), residues: 462 loop : -1.16 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 196 HIS 0.002 0.000 HIS G 83 PHE 0.012 0.001 PHE E 266 TYR 0.011 0.001 TYR H 49 ARG 0.002 0.000 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 18) link_NAG-ASN : angle 3.74338 ( 54) link_BETA1-4 : bond 0.00445 ( 14) link_BETA1-4 : angle 1.40707 ( 42) hydrogen bonds : bond 0.04257 ( 419) hydrogen bonds : angle 4.10851 ( 1167) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.14832 ( 24) covalent geometry : bond 0.00254 (12916) covalent geometry : angle 0.54196 (17664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7288 (m-70) cc_final: 0.7039 (m-70) REVERT: C 117 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7708 (ptt-90) REVERT: C 234 ASP cc_start: 0.7555 (t0) cc_final: 0.7229 (t0) REVERT: D 201 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: D 209 MET cc_start: 0.6212 (tpp) cc_final: 0.5484 (mtt) REVERT: A 57 LEU cc_start: 0.8208 (tp) cc_final: 0.7858 (mp) REVERT: G 246 TYR cc_start: 0.6191 (p90) cc_final: 0.5800 (p90) REVERT: H 201 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: H 209 MET cc_start: 0.6410 (tpp) cc_final: 0.6015 (mtt) REVERT: E 57 LEU cc_start: 0.8284 (tp) cc_final: 0.7818 (mp) outliers start: 39 outliers final: 29 residues processed: 142 average time/residue: 0.1872 time to fit residues: 43.1636 Evaluate side-chains 144 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS G 285 ASN H 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.186944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136162 restraints weight = 17519.743| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.76 r_work: 0.3487 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12960 Z= 0.117 Angle : 0.618 16.224 17784 Z= 0.288 Chirality : 0.048 0.577 2022 Planarity : 0.004 0.059 2228 Dihedral : 4.784 48.123 2340 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 14.86 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.56 (0.22), residues: 1514 helix: 3.74 (0.31), residues: 248 sheet: 0.86 (0.25), residues: 464 loop : -1.10 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 196 HIS 0.002 0.000 HIS D 52 PHE 0.015 0.002 PHE H 69 TYR 0.011 0.001 TYR H 49 ARG 0.002 0.000 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 18) link_NAG-ASN : angle 4.86067 ( 54) link_BETA1-4 : bond 0.00597 ( 14) link_BETA1-4 : angle 1.35755 ( 42) hydrogen bonds : bond 0.04597 ( 419) hydrogen bonds : angle 4.05974 ( 1167) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.11433 ( 24) covalent geometry : bond 0.00270 (12916) covalent geometry : angle 0.55372 (17664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7276 (m-70) cc_final: 0.7065 (m-70) REVERT: C 117 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7488 (ptt-90) REVERT: C 234 ASP cc_start: 0.7594 (t0) cc_final: 0.7266 (t0) REVERT: D 201 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: D 209 MET cc_start: 0.6171 (tpp) cc_final: 0.5450 (mtt) REVERT: A 57 LEU cc_start: 0.8218 (tp) cc_final: 0.7879 (mp) REVERT: G 246 TYR cc_start: 0.6131 (p90) cc_final: 0.5740 (p90) REVERT: H 201 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: H 209 MET cc_start: 0.6394 (tpp) cc_final: 0.6009 (mtt) REVERT: E 57 LEU cc_start: 0.8287 (tp) cc_final: 0.7827 (mp) outliers start: 39 outliers final: 27 residues processed: 143 average time/residue: 0.1906 time to fit residues: 43.4807 Evaluate side-chains 143 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 0.0000 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN D 106 ASN A 117 HIS G 83 HIS G 285 ASN H 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134866 restraints weight = 17449.757| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.69 r_work: 0.3470 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12960 Z= 0.117 Angle : 0.599 13.078 17784 Z= 0.283 Chirality : 0.047 0.527 2022 Planarity : 0.004 0.063 2228 Dihedral : 4.756 48.632 2340 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.64 % Allowed : 15.54 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.69 (0.23), residues: 1514 helix: 3.72 (0.31), residues: 248 sheet: 0.95 (0.24), residues: 482 loop : -1.01 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 196 HIS 0.002 0.000 HIS D 175 PHE 0.015 0.002 PHE H 69 TYR 0.010 0.001 TYR H 49 ARG 0.002 0.000 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 18) link_NAG-ASN : angle 4.19953 ( 54) link_BETA1-4 : bond 0.00545 ( 14) link_BETA1-4 : angle 1.24361 ( 42) hydrogen bonds : bond 0.04726 ( 419) hydrogen bonds : angle 4.01167 ( 1167) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.09937 ( 24) covalent geometry : bond 0.00270 (12916) covalent geometry : angle 0.54969 (17664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7225 (m-70) cc_final: 0.7022 (m-70) REVERT: C 117 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7470 (ptt-90) REVERT: C 234 ASP cc_start: 0.7615 (t0) cc_final: 0.7297 (t0) REVERT: D 201 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: D 209 MET cc_start: 0.6311 (tpp) cc_final: 0.5571 (mtt) REVERT: A 57 LEU cc_start: 0.8226 (tp) cc_final: 0.7888 (mp) REVERT: A 150 ASP cc_start: 0.8816 (p0) cc_final: 0.8549 (p0) REVERT: G 103 LEU cc_start: 0.5359 (pp) cc_final: 0.4709 (mm) REVERT: G 246 TYR cc_start: 0.6085 (p90) cc_final: 0.5736 (p90) REVERT: H 201 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: H 209 MET cc_start: 0.6435 (tpp) cc_final: 0.6048 (mtt) REVERT: E 57 LEU cc_start: 0.8289 (tp) cc_final: 0.7827 (mp) outliers start: 35 outliers final: 25 residues processed: 141 average time/residue: 0.1774 time to fit residues: 40.3672 Evaluate side-chains 137 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS G 100 GLN G 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130478 restraints weight = 17543.965| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.91 r_work: 0.3415 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.140 Angle : 0.625 13.014 17784 Z= 0.301 Chirality : 0.047 0.488 2022 Planarity : 0.004 0.058 2228 Dihedral : 4.855 47.248 2340 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.56 % Allowed : 16.29 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.64 (0.23), residues: 1514 helix: 3.72 (0.31), residues: 244 sheet: 0.83 (0.24), residues: 486 loop : -0.97 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 196 HIS 0.004 0.001 HIS A 117 PHE 0.013 0.002 PHE C 243 TYR 0.013 0.001 TYR C 87 ARG 0.003 0.000 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 18) link_NAG-ASN : angle 3.96236 ( 54) link_BETA1-4 : bond 0.00470 ( 14) link_BETA1-4 : angle 1.23474 ( 42) hydrogen bonds : bond 0.05570 ( 419) hydrogen bonds : angle 4.12803 ( 1167) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.19559 ( 24) covalent geometry : bond 0.00326 (12916) covalent geometry : angle 0.58320 (17664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7177 (m-70) cc_final: 0.6952 (m-70) REVERT: C 234 ASP cc_start: 0.7691 (t0) cc_final: 0.7364 (t0) REVERT: D 201 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: D 209 MET cc_start: 0.6387 (tpp) cc_final: 0.5647 (mtt) REVERT: A 57 LEU cc_start: 0.8285 (tp) cc_final: 0.7932 (mp) REVERT: A 150 ASP cc_start: 0.8803 (p0) cc_final: 0.8538 (p0) REVERT: G 103 LEU cc_start: 0.5354 (pp) cc_final: 0.4725 (mm) REVERT: G 246 TYR cc_start: 0.5950 (p90) cc_final: 0.5593 (p90) REVERT: H 201 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: H 209 MET cc_start: 0.6627 (tpp) cc_final: 0.6192 (mtt) REVERT: E 57 LEU cc_start: 0.8366 (tp) cc_final: 0.7893 (mp) REVERT: E 89 ARG cc_start: 0.6803 (mtm110) cc_final: 0.6587 (mtm110) outliers start: 34 outliers final: 23 residues processed: 138 average time/residue: 0.2079 time to fit residues: 46.2382 Evaluate side-chains 133 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS C 285 ASN E 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125175 restraints weight = 17578.781| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.12 r_work: 0.3326 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12960 Z= 0.192 Angle : 0.711 14.201 17784 Z= 0.346 Chirality : 0.050 0.516 2022 Planarity : 0.005 0.073 2228 Dihedral : 5.207 48.045 2340 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.19 % Allowed : 17.12 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.31 (0.22), residues: 1514 helix: 3.02 (0.32), residues: 256 sheet: 0.76 (0.24), residues: 476 loop : -1.18 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 196 HIS 0.005 0.001 HIS C 83 PHE 0.019 0.002 PHE C 243 TYR 0.017 0.002 TYR D 110 ARG 0.005 0.001 ARG D 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 18) link_NAG-ASN : angle 4.16764 ( 54) link_BETA1-4 : bond 0.00391 ( 14) link_BETA1-4 : angle 1.30924 ( 42) hydrogen bonds : bond 0.07091 ( 419) hydrogen bonds : angle 4.44736 ( 1167) SS BOND : bond 0.00367 ( 12) SS BOND : angle 1.46154 ( 24) covalent geometry : bond 0.00461 (12916) covalent geometry : angle 0.66972 (17664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7154 (m-70) cc_final: 0.6911 (m-70) REVERT: C 234 ASP cc_start: 0.7820 (t0) cc_final: 0.7406 (t0) REVERT: D 209 MET cc_start: 0.6549 (tpp) cc_final: 0.6055 (mtt) REVERT: A 57 LEU cc_start: 0.8350 (tp) cc_final: 0.7989 (mp) REVERT: A 150 ASP cc_start: 0.8837 (p0) cc_final: 0.8587 (p0) REVERT: G 103 LEU cc_start: 0.5376 (pp) cc_final: 0.4722 (mm) REVERT: G 246 TYR cc_start: 0.6007 (p90) cc_final: 0.5710 (p90) REVERT: H 201 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: H 209 MET cc_start: 0.6759 (tpp) cc_final: 0.6389 (mtt) REVERT: E 57 LEU cc_start: 0.8411 (tp) cc_final: 0.7959 (mp) REVERT: E 89 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6600 (mtm110) outliers start: 29 outliers final: 24 residues processed: 129 average time/residue: 0.2051 time to fit residues: 43.2072 Evaluate side-chains 124 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129054 restraints weight = 17699.099| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 4.19 r_work: 0.3380 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12960 Z= 0.127 Angle : 0.665 16.803 17784 Z= 0.317 Chirality : 0.051 0.773 2022 Planarity : 0.004 0.061 2228 Dihedral : 5.506 58.980 2340 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.04 % Allowed : 17.65 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.43 (0.22), residues: 1514 helix: 3.17 (0.32), residues: 256 sheet: 0.69 (0.24), residues: 484 loop : -1.04 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 PHE 0.012 0.001 PHE A 266 TYR 0.013 0.001 TYR H 49 ARG 0.003 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 18) link_NAG-ASN : angle 4.29222 ( 54) link_BETA1-4 : bond 0.00360 ( 14) link_BETA1-4 : angle 1.14198 ( 42) hydrogen bonds : bond 0.05680 ( 419) hydrogen bonds : angle 4.21484 ( 1167) SS BOND : bond 0.00389 ( 12) SS BOND : angle 1.25016 ( 24) covalent geometry : bond 0.00292 (12916) covalent geometry : angle 0.61908 (17664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7294.75 seconds wall clock time: 127 minutes 9.54 seconds (7629.54 seconds total)